Troubleshooting

What to try when a paper is missing, annotations or handwriting don't arrive, search misses something or Reading Mode looks wrong, and how to send us diagnostic data.

Applies to Mendeley and Zotero editions Windows · Mac · iPad Free

Nothing under Settings › Troubleshooting deletes your annotations, handwriting or PDFs. Clearing a cache or rebuilding an index only makes Rectoly work it out again.

A paper isn't in the list

  1. Check that the list isn't narrowed: pick All in the sidebar (or the view chips on Windows), clear any tag filter, and empty the search field.
  2. Sync the library. Papers you added in Mendeley or Zotero appear after a sync. See Syncing the library.
  3. The search field matches titles, authors and years. To find words inside papers or your notes, use Across papers. See Search.
  4. WindowsRectoly on Windows reads your library but doesn't edit it. Organize collections and tags in Mendeley Reference Manager or Zotero; the changes appear after the next sync.

"File not synced" Zotero edition

Zotero editionThe PDF is not in Zotero storage yet, so Rectoly can't download it. Sync the file from Zotero on your computer first. If your attachment files are on a WebDAV server, or ZotFile or ZotMoov moved them into a cloud folder, set that up in settings: see Files on a WebDAV server and Files linked with ZotFile or ZotMoov. See Downloading PDFs.

Annotations don't arrive

  • Press the sync button in the paper to send and fetch its annotations now. Library sync does not send annotations; each paper syncs its own.
  • Unsent annotations stay on the device and are retried automatically. If sending keeps failing, it pauses until you press sync again.
  • If the same annotation changed in two places, it becomes a conflict. Press the conflict count and choose which version to keep.

See Annotation sync, unsent and conflicts.

Handwriting doesn't appear on another device

Check on the device where you wrote it: the same account is signed in, the paper was opened from the library (not as a separate file), and handwriting sharing is on. Then sync the paper's annotations. The details differ by edition and by where you wrote; see Sharing handwriting between tablets and PCs.

Search misses a paper: rebuild the index

Search across papers only finds text in papers that were opened or indexed on this device. If results are missing, rebuild the index:

  • Mac · iPadSettings › Troubleshooting › Search index for Across papers › Rebuild.
  • WindowsSettings › Troubleshooting › Search index for Across papers › Rebuild.

Rectoly reads every PDF on the device again. Until it finishes, some papers can be missing from the results.

Reading Mode looks wrong: clear the structure cache

Rectoly keeps how it rebuilt each paper for Reading Mode. If a paper looks wrong after an update, clear this cache; each paper is rebuilt the next time it opens in Reading Mode.

  • Mac · iPadSettings › Troubleshooting › Paper structure cache › Clear structure cache.
  • WindowsSettings › Troubleshooting › Paper structure cache › Clear.

If the layout is still wrong, send it to us with Report a layout problem in the … menu on iPad and Mac. Only positions and structure are sent, with the text masked. See Reading Mode.

  • Zotero editionFor scanned papers, the recognized text can be cleared and read again. See Scanned PDFs.

"Sync paused to protect your data" Mac · iPad

Mac · iPadRectoly pauses iCloud sync when a large amount of data is about to change at once, to protect what you have. If you deleted things on purpose, choose I meant to delete these — resume sync. If not, choose Restore from iCloud backup. See iCloud backup.

Export diagnostic data

Diagnostic data helps us see what went wrong. You make the file yourself and decide whether to send it.

  • Mac · iPadSettings › Troubleshooting › Export diagnostic data. The zip is attached to an email to us, which you can review before sending (without a Mail account, the share sheet opens). It contains annotation files, the list of handwriting files and recent logs. PDFs and the handwriting itself are not included; annotation text is.
  • WindowsSettings › Troubleshooting › Export diagnostic data › Export…, then choose where to save the zip. It contains settings, sync state, annotation counts per paper and recent logs, but no annotation text, handwriting, PDFs or paper titles. Nothing is sent by itself.
  • WindowsConnection and storage check › Run diagnostics checks the connection to Mendeley or Zotero and to Rectoly. Copy results lets you paste them into an email. Open log folder shows the log files.

Contact us

Email rectoly.app@gmail.com, with the diagnostic data if you can. It helps to add:

  • what happened (for example, handwriting disappeared or sync stopped),
  • which paper and page it happened on,
  • roughly when it happened.

Replies may take a few days. Settings › About also has a Contact link.

Updated September 20, 2026