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Unfortunately when cancelling the sync, it can only be interrupted at certain stages as far as I'm aware, so it is normal for cancelling to continue some actions before it stops.
However, you were likely prompted to cancel the sync due to seeing many deletions, which is likely due to note history cleaning now working correctly in newer versions of Joplin (it did not work correctly for a long time). See #11488 for more information regarding this.
On Joplin desktop, go to Tools > Export deletion log. Here you can confirm what items were deleted in your sync yesterday, if they were in fact majority or entirely revisions. There is an equivalent log which can be viewed on the mobile app as well
Operating system
Linux
Joplin version
3.0.15
Desktop version info
Joplin 3.0.15 (prod , linux)
Current behaviour
Expected behaviour
Logs
Deleted remote items: 1077.
Completed: 2025-01-05 01:32 (3894s)
Last error: Sync target is locked - aborting API call
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