Annotation sync, unsent and conflicts

Rectoly exchanges your highlights, underlines and sticky notes with Mendeley or Zotero, so your computer and your other devices show the same annotations.

Applies to Mendeley and Zotero editions Windows · Mac · iPad Partly included in the purchase

Syncing happens by itself

Usually there is nothing to do. Rectoly syncs a paper's annotations when you open it, when you change something, and from time to time while you read.

  • WindowsIt also syncs every five minutes.

Handwriting has its own rules — see Sharing handwriting between tablets and PCs.

Sending annotations to Mendeley or Zotero is included in the purchase. It is free during the 14-day trial and inside the sample paper. Your annotations always stay on your device. See Trial and purchase.

Sync now

  • Mac · iPadChoose the Sync tool, or press the sync count in the status bar.
  • WindowsClick the sync button above the paper (Sync annotations with Mendeley / Sync annotations with Zotero).

What the status means

  • Mac · iPadThe status bar shows the number of annotations, and Unsent and Conflict counts when there are any.
  • WindowsYou see "Synced with Mendeley" (or Zotero) when all is sent, and "N unsent" while something is waiting.

Unsent annotations

If an annotation cannot be sent — no connection, or Mendeley or Zotero does not answer — it stays on your device as unsent. Nothing is lost.

  1. Rectoly tries again by itself ("Retrying in N s").
  2. After several failed tries it pauses. Press sync to try again.
    • WindowsThe banner "N annotations could not be sent…" has Send now.
  3. Once it goes through, the unsent count disappears.

Annotations you create, change or delete while a sync is running are kept; the sync does not overwrite them.

Conflicts

A conflict happens when the same annotation was changed here and somewhere else (in Mendeley or Zotero, or on another device) before the two could sync — or deleted in one place and edited in the other.

  1. Open the conflict:
    • Mac · iPadPress the Conflict count, or open the reader's settings and choose Resolve conflicts….
    • WindowsIn the side panel's annotation list, open the annotation marked Conflict.
  2. Choose which version to keep:
    • Keep Local keeps the version on this device.
    • Use Remote uses the other version.
    • WindowsIf it was deleted on the other side: Accept deletion or Recreate Mine.
    • Mac · iPadKeep both keeps the two versions.
    • WindowsFor a duplicate made in the same place: Merge, keep mine.

What you chose is recorded in the annotation's history.

When the PDF file changes

If the PDF attached in Mendeley or Zotero is replaced by a new version, Rectoly moves your annotations onto the new pages and tells you how many it moved ("The PDF changed: moved N annotations to the new version"). Annotations whose place could not be found are counted separately.

  • Zotero editionIn the Zotero edition the moved positions are also sent to Zotero.

Zotero groups

  • Zotero editionAnnotations on papers in a Zotero group sync when your role in the group is owner, admin or member.
  • WindowsZotero editionIf Zotero refuses a change — a read-only group, a full storage quota, or an expired key — Rectoly tells you the reason.

Updated September 20, 2026