diff --git a/services/web/scripts/fix_malformed_filetree.mjs b/services/web/scripts/fix_malformed_filetree.mjs
index 5e12c3cb77..491da4762d 100644
--- a/services/web/scripts/fix_malformed_filetree.mjs
+++ b/services/web/scripts/fix_malformed_filetree.mjs
@@ -140,7 +140,10 @@ function parentPath(path) {
  */
 async function fixRootFolder(projectId) {
   const result = await db.projects.updateOne(
-    { _id: projectId, rootFolder: [] },
+    {
+      _id: new ObjectId(projectId),
+      rootFolder: { $size: 0 },
+    },
     {
       $set: {
         rootFolder: [
@@ -163,7 +166,7 @@ async function fixRootFolder(projectId) {
  */
 async function removeNulls(projectId, path) {
   const result = await db.projects.updateOne(
-    { _id: projectId, [path]: { $type: 'array' } },
+    { _id: new ObjectId(projectId), [path]: { $type: 'array' } },
     { $pull: { [path]: null } }
   )
   return result.modifiedCount
@@ -174,7 +177,7 @@ async function removeNulls(projectId, path) {
  */
 async function fixArray(projectId, path) {
   const result = await db.projects.updateOne(
-    { _id: projectId, [path]: { $not: { $type: 'array' } } },
+    { _id: new ObjectId(projectId), [path]: { $not: { $type: 'array' } } },
     { $set: { [path]: [] } }
   )
   return result.modifiedCount
@@ -185,7 +188,7 @@ async function fixArray(projectId, path) {
  */
 async function fixFolderId(projectId, path) {
   const result = await db.projects.updateOne(
-    { _id: projectId, [path]: { $exists: false } },
+    { _id: new ObjectId(projectId), [path]: { $exists: false } },
     { $set: { [path]: new ObjectId() } }
   )
   return result.modifiedCount
@@ -196,7 +199,7 @@ async function fixFolderId(projectId, path) {
  */
 async function removeElementsWithoutIds(projectId, path) {
   const result = await db.projects.updateOne(
-    { _id: projectId, [path]: { $type: 'array' } },
+    { _id: new ObjectId(projectId), [path]: { $type: 'array' } },
     { $pull: { [path]: { _id: null } } }
   )
   return result.modifiedCount
@@ -207,15 +210,16 @@ async function removeElementsWithoutIds(projectId, path) {
  */
 async function fixName(projectId, path) {
   const project = await db.projects.findOne(
-    { _id: projectId },
+    { _id: new ObjectId(projectId) },
     { projection: { rootFolder: 1 } }
   )
   const arrayPath = parentPath(parentPath(path))
   const array = ProjectLocator.findElementByMongoPath(project, arrayPath)
   const existingNames = new Set(array.map(x => x.name))
-  const name = findUniqueName(existingNames)
+  const name =
+    path === 'rootFolder.0.name' ? 'rootFolder' : findUniqueName(existingNames)
   const result = await db.projects.updateOne(
-    { _id: projectId, [path]: { $in: [null, ''] } },
+    { _id: new ObjectId(projectId), [path]: { $in: [null, ''] } },
     { $set: { [path]: name } }
   )
   return result.modifiedCount
diff --git a/services/web/test/acceptance/src/DeleteOrphanedDocsOnlineCheckTests.mjs b/services/web/test/acceptance/src/DeleteOrphanedDocsOnlineCheckTests.mjs
index 748561613a..fc69d7750a 100644
--- a/services/web/test/acceptance/src/DeleteOrphanedDocsOnlineCheckTests.mjs
+++ b/services/web/test/acceptance/src/DeleteOrphanedDocsOnlineCheckTests.mjs
@@ -160,7 +160,6 @@ describe('DeleteOrphanedDocsOnlineCheck', function () {
       `Deleted project ${projectIds[8]} has 1 orphaned docs: ["${docIds[8]}"]`,
       // Two docs in the same project
       `Deleted project ${projectIds[9]} has 2 orphaned docs: ["${docIds[9]}","${docIds[10]}"]`,
-      '',
     ])
     expect(stdErr).to.deep.equal([
       ...`Options: ${JSON.stringify(options, null, 2)}`.split('\n'),
@@ -219,7 +218,6 @@ describe('DeleteOrphanedDocsOnlineCheck', function () {
       // 10 has as ready been processed as part of the last batch -- same project_id as 9.
       `Processed 10 projects (8 projects with orphaned docs/10 docs deleted) until ${oneDayFromProjectId9AsObjectId}`,
       'Done.',
-      '',
     ])
   }
 
diff --git a/services/web/test/acceptance/src/MalformedFiletreesTests.mjs b/services/web/test/acceptance/src/MalformedFiletreesTests.mjs
new file mode 100644
index 0000000000..d1dd8ea937
--- /dev/null
+++ b/services/web/test/acceptance/src/MalformedFiletreesTests.mjs
@@ -0,0 +1,567 @@
+import { exec } from 'node:child_process'
+import { promisify } from 'node:util'
+import { expect } from 'chai'
+import logger from '@overleaf/logger'
+import { filterOutput } from './helpers/settings.mjs'
+import { db, ObjectId } from '../../../app/src/infrastructure/mongodb.js'
+
+async function runScriptFind() {
+  try {
+    const result = await promisify(exec)(
+      ['node', 'scripts/find_malformed_filetrees.mjs'].join(' ')
+    )
+    return result.stdout.split('\n').filter(filterOutput)
+  } catch (error) {
+    logger.error({ error }, 'script failed')
+    throw error
+  }
+}
+
+async function runScriptFix(instructions) {
+  const adhocFile = instructions.map(entry => JSON.stringify(entry)).join('\n')
+  try {
+    return await promisify(exec)(
+      [
+        'node',
+        'scripts/fix_malformed_filetree.mjs',
+        `--logs=<(echo '${adhocFile}')`,
+      ].join(' '),
+      { shell: '/bin/bash' }
+    )
+  } catch (error) {
+    logger.error({ error }, 'fix script failed unexpectedly')
+    throw error
+  }
+}
+
+const findProjects = () =>
+  db.projects
+    .find({}, { projection: { rootFolder: 1, _id: 1, version: 1 } })
+    .toArray()
+
+const projectId = new ObjectId()
+const rootFolderId = new ObjectId()
+
+const idDic = {}
+
+const id = key => {
+  if (!idDic[key]) {
+    idDic[key] = new ObjectId()
+  }
+  return idDic[key]
+}
+const strId = key => {
+  return idDic[key].toString()
+}
+
+const wellFormedFolder = name => ({
+  _id: id(name),
+  name,
+  folders: [],
+  docs: [],
+  fileRefs: [],
+})
+const wellFormedDoc = name => ({ _id: id(name), name })
+const wellFormedFileRef = name => ({ _id: id(name), name, hash: 'h' })
+
+const wellFormedProject = {
+  _id: projectId,
+  rootFolder: [
+    {
+      _id: rootFolderId,
+      name: 'rootFolder',
+      folders: [wellFormedFolder('f00'), wellFormedFolder('f01')],
+      docs: [wellFormedDoc('d00'), wellFormedDoc('d01')],
+      fileRefs: [wellFormedFileRef('fr00'), wellFormedFileRef('fr01')],
+    },
+  ],
+}
+
+const testCases = [
+  ...[{}, { rootFolder: undefined }, { rootFolder: '1234' }].map(
+    (project, idx) => ({
+      name: `bad rootFolder ${idx + 1}`,
+      project: { _id: projectId, ...project },
+      expectFind: [
+        {
+          _id: null,
+          projectId: projectId.toString(),
+          msg: 'bad file-tree path',
+          reason: 'bad rootFolder',
+          path: 'rootFolder',
+        },
+      ],
+      // FIXME: This is a bug in the script.
+      expectFixError: 'Unexpected mongo path: rootFolder',
+    })
+  ),
+
+  {
+    name: `missing rootFolder`,
+    project: { _id: projectId, rootFolder: [] },
+    expectFind: [
+      {
+        _id: null,
+        projectId: projectId.toString(),
+        msg: 'bad file-tree path',
+        reason: 'missing rootFolder',
+        path: 'rootFolder.0',
+      },
+    ],
+    expectFixStdout:
+      '"gracefulShutdownInitiated":false,"processedLines":1,"success":1,"alreadyProcessed":0,"hash":0,"failed":0,"unmatched":0',
+    expectProject: updatedProject => {
+      expect(updatedProject.rootFolder[0]._id).to.be.an.instanceOf(ObjectId)
+      expect(updatedProject).to.deep.equal({
+        _id: projectId,
+        rootFolder: [
+          {
+            _id: updatedProject.rootFolder[0]._id,
+            name: 'rootFolder',
+            folders: [],
+            fileRefs: [],
+            docs: [],
+          },
+        ],
+      })
+    },
+  },
+
+  {
+    name: 'empty folder',
+    project: {
+      _id: projectId,
+      rootFolder: [{ _id: '1234' }],
+    },
+    expectFind: [
+      { reason: 'bad folder id', path: 'rootFolder.0._id' },
+      { reason: 'bad folder name', path: 'rootFolder.0.name' },
+      { reason: 'missing .folders', path: 'rootFolder.0.folders' },
+      { reason: 'missing .docs', path: 'rootFolder.0.docs' },
+      { reason: 'missing .fileRefs', path: 'rootFolder.0.fileRefs' },
+    ].map(entry => ({
+      ...entry,
+      _id: '1234',
+      msg: 'bad file-tree path',
+      projectId: String(projectId),
+    })),
+    // FIXME: This is a bug in the script.
+    expectFixError: 'Unexpected mongo path: rootFolder.0._id',
+  },
+
+  {
+    name: 'missing fields',
+    project: {
+      _id: projectId,
+      rootFolder: [{ _id: rootFolderId }],
+    },
+    expectFind: [
+      { reason: 'bad folder name', path: 'rootFolder.0.name' },
+      { reason: 'missing .folders', path: 'rootFolder.0.folders' },
+      { reason: 'missing .docs', path: 'rootFolder.0.docs' },
+      { reason: 'missing .fileRefs', path: 'rootFolder.0.fileRefs' },
+    ].map(entry => ({
+      ...entry,
+      _id: rootFolderId.toString(),
+      msg: 'bad file-tree path',
+      projectId: String(projectId),
+    })),
+    expectFixStdout:
+      '"gracefulShutdownInitiated":false,"processedLines":4,"success":4,"alreadyProcessed":0,"hash":0,"failed":0,"unmatched":0',
+    expectProject: updatedProject => {
+      expect(updatedProject).to.deep.equal({
+        _id: projectId,
+        rootFolder: [
+          {
+            _id: rootFolderId,
+            docs: [],
+            fileRefs: [],
+            folders: [],
+            name: 'rootFolder',
+          },
+        ],
+      })
+    },
+  },
+
+  {
+    name: 'bad folder, bad doc, bad fileRef',
+    project: {
+      _id: projectId,
+      rootFolder: [
+        {
+          _id: rootFolderId,
+          name: 'rootFolder',
+          folders: [null],
+          docs: [null],
+          fileRefs: [null, null],
+        },
+      ],
+    },
+    expectFind: [
+      {
+        path: 'rootFolder.0.folders.0',
+        reason: 'bad folder',
+      },
+      {
+        path: 'rootFolder.0.docs.0',
+        reason: 'bad doc',
+      },
+      {
+        path: 'rootFolder.0.fileRefs.0',
+        reason: 'bad file',
+      },
+      {
+        path: 'rootFolder.0.fileRefs.1',
+        reason: 'bad file',
+      },
+    ].map(entry => ({
+      ...entry,
+      _id: rootFolderId.toString(),
+      projectId: projectId.toString(),
+      msg: 'bad file-tree path',
+    })),
+    expectFixStdout:
+      '"gracefulShutdownInitiated":false,"processedLines":4,"success":3,"alreadyProcessed":1,"hash":0,"failed":0,"unmatched":0',
+    expectProject: updatedProject => {
+      expect(updatedProject).to.deep.equal({
+        _id: projectId,
+        rootFolder: [
+          {
+            _id: rootFolderId,
+            name: 'rootFolder',
+            docs: [],
+            fileRefs: [],
+            folders: [],
+          },
+        ],
+      })
+    },
+  },
+
+  {
+    name: 'bad [folder|doc|fileRef] id',
+    project: {
+      _id: projectId,
+      rootFolder: [
+        {
+          _id: rootFolderId,
+          name: 'rootFolder',
+          folders: [
+            { _id: 123, name: 'file-a', folders: [], docs: [], fileRefs: [] },
+            { name: 'file-b', folders: [], docs: [], fileRefs: [] },
+          ],
+          docs: [{ _id: '456', name: 'doc-a' }, { name: 'doc-b' }],
+          fileRefs: [{ _id: null, name: 'ref-a' }, { name: 'ref-b' }],
+        },
+      ],
+    },
+    expectFind: [
+      { reason: 'bad folder id', path: 'rootFolder.0.folders.0._id', _id: 123 },
+      { reason: 'bad folder id', path: 'rootFolder.0.folders.1._id' },
+      { reason: 'bad doc id', path: 'rootFolder.0.docs.0._id', _id: '456' },
+      { reason: 'bad doc id', path: 'rootFolder.0.docs.1._id' },
+      { reason: 'bad file id', path: 'rootFolder.0.fileRefs.0._id', _id: null },
+      { reason: 'bad file id', path: 'rootFolder.0.fileRefs.1._id' },
+    ].map(entry => ({
+      ...entry,
+      projectId: projectId.toString(),
+      msg: 'bad file-tree path',
+    })),
+    expectFixStdout:
+      '"gracefulShutdownInitiated":false,"processedLines":6,"success":3,"alreadyProcessed":3,"hash":0,"failed":0,"unmatched":0',
+    expectProject: updatedProject => {
+      expect(updatedProject).to.deep.equal({
+        _id: projectId,
+        rootFolder: [
+          {
+            _id: rootFolderId,
+            name: 'rootFolder',
+            folders: [
+              { _id: 123, name: 'file-a', folders: [], docs: [], fileRefs: [] },
+              {
+                _id: updatedProject.rootFolder[0].folders[1]._id,
+                name: 'file-b',
+                folders: [],
+                docs: [],
+                fileRefs: [],
+              },
+            ],
+            docs: [{ _id: '456', name: 'doc-a' }],
+            fileRefs: [],
+          },
+        ],
+      })
+    },
+  },
+
+  {
+    name: 'bad [folder|doc|fileRef] name',
+    project: {
+      _id: projectId,
+      rootFolder: [
+        {
+          _id: rootFolderId,
+          name: 'rootFolder',
+          folders: [
+            { _id: id('f00'), folders: [], docs: [], fileRefs: [] },
+            { _id: id('f01'), name: 8, folders: [], docs: [], fileRefs: [] },
+          ],
+          docs: [{ _id: id('d00') }, { _id: id('d01'), name: null }],
+          fileRefs: [
+            { _id: id('fr00'), hash: 'h' },
+            { _id: id('fr01'), hash: 'h', name: [] },
+          ],
+        },
+      ],
+    },
+    expectFind: [
+      {
+        reason: 'bad folder name',
+        path: 'rootFolder.0.folders.0.name',
+        _id: strId('f00'),
+      },
+      {
+        reason: 'bad folder name',
+        path: 'rootFolder.0.folders.1.name',
+        _id: strId('f01'),
+      },
+      {
+        reason: 'bad doc name',
+        path: 'rootFolder.0.docs.0.name',
+        _id: strId('d00'),
+      },
+      {
+        reason: 'bad doc name',
+        path: 'rootFolder.0.docs.1.name',
+        _id: strId('d01'),
+      },
+      {
+        reason: 'bad file name',
+        path: 'rootFolder.0.fileRefs.0.name',
+        _id: strId('fr00'),
+      },
+      {
+        reason: 'bad file name',
+        path: 'rootFolder.0.fileRefs.1.name',
+        _id: strId('fr01'),
+      },
+    ].map(entry => ({
+      ...entry,
+      projectId: projectId.toString(),
+      msg: 'bad file-tree path',
+    })),
+    expectFixStdout:
+      '"gracefulShutdownInitiated":false,"processedLines":6,"success":6,"alreadyProcessed":0,"hash":0,"failed":0,"unmatched":0',
+    expectProject: updatedProject => {
+      expect(updatedProject).to.deep.equal({
+        _id: projectId,
+        rootFolder: [
+          {
+            _id: rootFolderId,
+            name: 'rootFolder',
+            folders: [
+              {
+                _id: id('f00'),
+                name: 'untitled',
+                folders: [],
+                docs: [],
+                fileRefs: [],
+              },
+              {
+                _id: id('f01'),
+                name: 'untitled-1',
+                folders: [],
+                docs: [],
+                fileRefs: [],
+              },
+            ],
+            docs: [
+              { _id: id('d00'), name: 'untitled' },
+              { _id: id('d01'), name: 'untitled-1' },
+            ],
+            fileRefs: [
+              { _id: id('fr00'), hash: 'h', name: 'untitled' },
+              { _id: id('fr01'), hash: 'h', name: 'untitled-1' },
+            ],
+          },
+        ],
+      })
+    },
+  },
+
+  {
+    name: 'bad file hash',
+    project: {
+      ...wellFormedProject,
+      rootFolder: [
+        {
+          ...wellFormedProject.rootFolder[0],
+          fileRefs: [
+            { _id: id('fa'), name: 'ref-a', hash: null },
+            { _id: id('fb'), name: 'ref-b', hash: {} },
+          ],
+        },
+      ],
+    },
+    expectFind: [
+      { path: 'rootFolder.0.fileRefs.0.hash', _id: strId('fa') },
+      { path: 'rootFolder.0.fileRefs.1.hash', _id: strId('fb') },
+    ].map(entry => ({
+      ...entry,
+      projectId: projectId.toString(),
+      reason: 'bad file hash',
+      msg: 'bad file-tree path',
+    })),
+    expectFixError: new RegExp(
+      `Missing file hash: ${projectId.toString()}/${id('fa').toString()}`
+    ),
+  },
+
+  {
+    name: 'well formed filetrees',
+    project: wellFormedProject,
+    expectFind: [],
+    expectFixStdout:
+      '"gracefulShutdownInitiated":false,"processedLines":1,"success":0,"alreadyProcessed":0,"hash":0,"failed":0,"unmatched":0',
+    expectProject: updatedProject => {
+      expect(updatedProject).to.deep.equal(wellFormedProject)
+    },
+  },
+
+  {
+    name: 'bug: shifted arrays in filetree',
+    project: {
+      _id: projectId,
+      rootFolder: [
+        {
+          _id: rootFolderId,
+          name: 'rootFolder',
+          folders: [null, null, { ...wellFormedFolder('f02'), name: null }],
+          docs: [null, null, { ...wellFormedDoc('d02'), name: null }],
+          fileRefs: [null, null, { ...wellFormedFileRef('fr02'), name: null }],
+        },
+      ],
+    },
+    expectFind: [
+      {
+        _id: rootFolderId.toString(),
+        path: 'rootFolder.0.folders.0',
+        reason: 'bad folder',
+      },
+      {
+        _id: rootFolderId.toString(),
+        path: 'rootFolder.0.folders.1',
+        reason: 'bad folder',
+      },
+      {
+        _id: strId('f02'),
+        path: 'rootFolder.0.folders.2.name',
+        reason: 'bad folder name',
+      },
+      {
+        _id: rootFolderId.toString(),
+        path: 'rootFolder.0.docs.0',
+        reason: 'bad doc',
+      },
+      {
+        _id: rootFolderId.toString(),
+        path: 'rootFolder.0.docs.1',
+        reason: 'bad doc',
+      },
+      {
+        _id: strId('d02'),
+        path: 'rootFolder.0.docs.2.name',
+        reason: 'bad doc name',
+      },
+      {
+        _id: rootFolderId.toString(),
+        path: 'rootFolder.0.fileRefs.0',
+        reason: 'bad file',
+      },
+      {
+        _id: rootFolderId.toString(),
+        path: 'rootFolder.0.fileRefs.1',
+        reason: 'bad file',
+      },
+      {
+        _id: strId('fr02'),
+        path: 'rootFolder.0.fileRefs.2.name',
+        reason: 'bad file name',
+      },
+    ].map(entry => ({
+      ...entry,
+      projectId: projectId.toString(),
+      msg: 'bad file-tree path',
+    })),
+    expectFixStdout:
+      '"gracefulShutdownInitiated":false,"processedLines":9,"success":6,"alreadyProcessed":3,"hash":0,"failed":0,"unmatched":0',
+    expectProject: updatedProject => {
+      expect(updatedProject).to.deep.equal({
+        _id: projectId,
+        rootFolder: [
+          {
+            _id: rootFolderId,
+            name: 'rootFolder',
+            // FIXME: The 3 arrays should only contain 1 item: the well-formed item with the name 'untitled'.
+            folders: [
+              { ...wellFormedFolder('f02'), name: null },
+              null,
+              { name: 'untitled' },
+            ],
+            docs: [
+              { ...wellFormedDoc('d02'), name: null },
+              null,
+              { name: 'untitled' },
+            ],
+            fileRefs: [
+              { ...wellFormedFileRef('fr02'), name: null },
+              null,
+              { name: 'untitled' },
+            ],
+          },
+        ],
+      })
+    },
+  },
+]
+
+describe('find_malformed_filetrees and fix_malformed_filetree scripts', function () {
+  testCases.forEach(
+    ({
+      name,
+      project,
+      expectFind,
+      expectFixStdout,
+      expectFixError,
+      expectProject,
+    }) => {
+      describe(name, function () {
+        beforeEach(async function () {
+          await db.projects.insertOne(project)
+        })
+
+        it('finds malformed filetree', async function () {
+          const stdout = await runScriptFind()
+          expect(stdout.map(line => JSON.parse(line))).to.deep.equal(expectFind)
+        })
+
+        if (expectFixError) {
+          it('fails to fix malformed filetrees', async function () {
+            await expect(runScriptFix(expectFind)).to.be.rejectedWith(
+              expectFixError
+            )
+          })
+        } else {
+          it('fixes malformed filetrees', async function () {
+            const { stdout } = await runScriptFix(expectFind)
+            expect(expectFixStdout).to.be.a('string')
+            expect(stdout).to.include(expectFixStdout)
+            const [updatedProject] = await findProjects()
+            expectProject(updatedProject)
+          })
+        }
+      })
+    }
+  )
+})
diff --git a/services/web/test/acceptance/src/RegenerateDuplicateReferralIdsTests.mjs b/services/web/test/acceptance/src/RegenerateDuplicateReferralIdsTests.mjs
index 2f54a03043..801ebfd455 100644
--- a/services/web/test/acceptance/src/RegenerateDuplicateReferralIdsTests.mjs
+++ b/services/web/test/acceptance/src/RegenerateDuplicateReferralIdsTests.mjs
@@ -117,7 +117,6 @@ describe('RegenerateDuplicateReferralIds', function () {
       `Completed batch ending ${renderObjectId(thirdBatch[BATCH_SIZE - 1])}`,
       `Completed batch ending ${renderObjectId(forthBatch[BATCH_SIZE - 1])}`,
       'Done.',
-      '',
     ])
     expect(stdOut.filter(filterOutput)).to.include.members([
       // only duplicates
@@ -137,7 +136,6 @@ describe('RegenerateDuplicateReferralIds', function () {
 
       // no new duplicates
       `Running update on batch with ids ${JSON.stringify(forthBatch)}`,
-      '',
     ])
   })
 
diff --git a/services/web/test/acceptance/src/helpers/settings.mjs b/services/web/test/acceptance/src/helpers/settings.mjs
index 7a0baafa71..9d92dc8edb 100644
--- a/services/web/test/acceptance/src/helpers/settings.mjs
+++ b/services/web/test/acceptance/src/helpers/settings.mjs
@@ -1,5 +1,6 @@
 export function filterOutput(line) {
   return (
+    !!line &&
     !line.startsWith('Using settings from ') &&
     !line.startsWith('Using default settings from ') &&
     !line.startsWith('CoffeeScript settings file') &&