iOS Joplin App Loses Sub-Notebooks After Multiple Syncs, Breaking Diary Navigation

Support
1

Operating system

iOS

Joplin version

13.3.7

Desktop version info

Joplin 3.2.13 (prod, win32)

Client ID: a5f4dc5ef198419e8ca9ee313d88dbb6
Sync Version：3
Profile Version：47
Keychain Supported：No

Revision：a898e17

Backup: 1.4.2
Freehand Drawing: 2.14.0
Templates: 2.4.0

Sync target

OneDrive

What issue do you have?

Dear Joplin Team,

Thank you for your outstanding work on Joplin, which I use daily for note-taking across platforms.

:magnifying_glass_tilted_left: Problem Description:
My diary notebooks are organized in a two-level hierarchy:

First, users navigate by clicking the parent notebook;

Then click the sub-notebook nested under it;

Finally, select the notes (diary entries) inside the sub-notebook.

Example structure:

  • 2025 Diaries (Parent Notebook)
    • January (Sub-Notebook)
      • Entry 1
      • Entry 2
    • February (Sub-Notebook)
      • Entry 3
        This hierarchical structure syncs correctly initially between Windows desktop and iOS Joplin apps.

Issue observed on iOS:

After multiple syncs over time, the sub-notebooks suddenly disappear from the iOS app’s interface. Only the parent notebooks remain visible.

This breaks the normal navigation path (parent notebook → sub-notebook → note), making it impossible to browse diary notes in their original organized folders.

Despite the disappearance of sub-notebooks in the UI, all notes remain intact and are still accessible under “All Notes.”

However, without the sub-notebook level, the tree structure is lost, and finding or browsing notes becomes inconvenient.

Attempts to move notes back to sub-notebooks (which still appear in the “Move to notebook” dialog) have no visible effect.

Reinstalling the iOS app and syncing temporarily resolves the issue, but it reoccurs after a few syncs.

This issue does not occur on the Windows version; the sub-notebook structure remains stable there.

:red_question_mark: Questions:

Is this a known bug or limitation in the iOS Joplin app regarding nested notebook persistence?

Are there plans to improve the reliability of sub-notebook syncing and display in future iOS releases?

Should users avoid using sub-notebooks on iOS for now until this is fixed?

Thank you again for your dedication to this great open-source tool. I look forward to your guidance and possible fixes.

Best regards,
lingd

2

Hi Lingd, a very similar problem here. I downloaded Joplin (v13.3.7) onto a new iPad this morning from the Appstore, entered the sync and encryption credentials and started syncing. To my big surprise, the iOS Joplin app started downloading a few notes (less than 10%) THEN deleted ALL my notes on the sync target, and reported "success". Checked all settings, couldn't find any problem.

So I closed it, went back to my desktop, opened Joplin (v3.3.12) and uploaded all my notes back onto the sync target. No problem. Went back to the iOS app, tried again ... and it started again deleting all notes on the sync target. That's about when I gave up as I don't have time to deal with it this weekend.

3

Hi everyone,
I’ve just updated the original post with a more detailed and accurate description of the issue. Thanks so much for your previous help and looking forward to any further insights!