# Notes and Notebooks Disappeared

**URL:** <https://discourse.joplinapp.org/t/notes-and-notebooks-disappeared/43168>\
**Category:** Support\
**Created:** [18 January 2025 00:47 UTC](https://discourse.joplinapp.org/t/notes-and-notebooks-disappeared/43168 "2025-01-18T00:47:01Z")\
**Posts on this page:** 9\
**Page:** 1

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**Author:** ![entomonkey](https://avatars.discourse-cdn.com/v4/letter/e/c37758/32.png) [@entomonkey](https://discourse.joplinapp.org/u/entomonkey)\
**Post date:** [18 January 2025 00:47 UTC](https://discourse.joplinapp.org/t/notes-and-notebooks-disappeared/43168/1 "2025-01-18T00:47:01Z")

</div>

### Operating system

Linux

### Joplin version

3.2.11

### Desktop version info

3.2.11

### What issue do you have?

I left my computer for a few minutes with Joplin open and when I came back and tried to start working, suddenly all my notes and notebooks disappeared. Two notes appeared in a new section called "Conflicts." I hadn't even touched the keyboard yet and my cat was with me the whole time, so it wasn't him.

I looked at the folder it syncs to and there are 359 files in it.

I don't use any cloud services for my notes.

Joplin is installed via Flatpak. (yes, I know this isn't an official version, but I hate AppImages and compiling things from source)

I exported the deletion log and all of my notes and files are listed there except for the two in "Conflicts." They all start with "2025-01-17 17:11:54: DeleteAction: sync:" except for one, which starts with "2025-01-16 20:33:58: DeleteAction: Revision.deleteOldRevisions:."

There was a message in the bottom left above the Synchronise button that said that five files were going to be deleted if I didn't disable "fail-safe" in the settings. (so I did, but none of my files have been returned)

What do I do? Why did this happen?

---

<div class="post-metadata">

**Author:** ![personalizedrefriger](https://yyz2.discourse-cdn.com/flex028/user_avatar/discourse.joplinapp.org/personalizedrefriger/32/13210_2.png) [@personalizedrefriger](https://discourse.joplinapp.org/u/personalizedrefriger)\
**Post date:** [18 January 2025 01:05 UTC](https://discourse.joplinapp.org/t/notes-and-notebooks-disappeared/43168/2 "2025-01-18T01:05:44Z")

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> [@entomonkey](#):
>
> I looked at the folder it syncs to and there are 359 files in it.

Hi,

I suggest 1) making a backup copy of the sync folder to prevent further issues, then 2) checking for backups created by the [built-in backup plugin](https://joplinapp.org/plugins/plugin/io.github.jackgruber.backup/).

By default, the backup plugin stores an automatic backup (updated roughly every 24 hours) in `~/JoplinBackup`. The Flatpak's backup plugin might store backups in a different location. The [backup plugin's README](https://joplinapp.org/plugins/plugin/io.github.jackgruber.backup/#restore) includes instructions for restoring from a backup.

---

<div class="post-metadata">

**Author:** ![entomonkey](https://avatars.discourse-cdn.com/v4/letter/e/c37758/32.png) [@entomonkey](https://discourse.joplinapp.org/u/entomonkey)\
**Post date:** [18 January 2025 01:15 UTC](https://discourse.joplinapp.org/t/notes-and-notebooks-disappeared/43168/3 "2025-01-18T01:15:33Z")

</div>

The backup plugin does not seem to be installed.

After locating the Flatpak directory for Joplin, there are several files each of the following names:

- backup.h
- simpleBackup.spec.js
- simpleBackup.spec.js.map
- simpleBackup.spec.ts

---

<div class="post-metadata">

**Author:** ![personalizedrefriger](https://yyz2.discourse-cdn.com/flex028/user_avatar/discourse.joplinapp.org/personalizedrefriger/32/13210_2.png) [@personalizedrefriger](https://discourse.joplinapp.org/u/personalizedrefriger)\
**Post date:** [18 January 2025 01:39 UTC](https://discourse.joplinapp.org/t/notes-and-notebooks-disappeared/43168/4 "2025-01-18T01:39:32Z")

</div>

> [@entomonkey](#):
>
> The backup plugin does not seem to be installed.

> **The Flatpak seems to disable building/including the backup plugin**
>
> > <https://github.com/flathub/net.cozic.joplin_desktop/blob/d32e3fd6f31ad039fbdba25e7e6bcf9e023a71b9/net.cozic.joplin_desktop.yml#L122>

> [@entomonkey](#):
>
> What do I do? Why did this happen?

Here are two things to try (after creating a backup copy of the sync directory):

1. Create a new profile and verify that file system sync works with a new local directory.
  - Below the "Directory to synchronize with" message, Joplin states:  
 ![Attention: If you change this location, make sure you copy all your content to it before syncing, otherwise all files will be removed! See the FAQ for more details: https://joplinapp.org/help/faq](https://canada1.discourse-cdn.com/flex028/uploads/cozic/original/3X/f/8/f80a47c030972ed36b0b1b461674fb634ace2246.png)  
Based on this, one possibility is that the Flatpak has lost permission to sync with the directory (or instead thinks the directory is different/empty).
  - If Joplin can't sync with a similar directory from a new profile, this suggests that it might be a permissions issue. The Flatpak's README includes information for [resolving permissions issues with file system sync and removable media](https://github.com/flathub/net.cozic.joplin_desktop/tree/master), which might be applicable to this issue.

2. Set up file system sync in a different distribution of Joplin (e.g. the [AppImage](https://github.com/laurent22/joplin/releases/tag/v3.2.11), [Snap](https://github.com/JGCarroll/joplin-desktop-snap), [deb](https://github.com/laurent22/joplin/releases/tag/v3.2.11), or [web version](https://github.com/joplin/web-app)), then export to JEX. Next, import the JEX in the Flatpak version of Joplin.

---

<div class="post-metadata">

**Author:** ![entomonkey](https://avatars.discourse-cdn.com/v4/letter/e/c37758/32.png) [@entomonkey](https://discourse.joplinapp.org/u/entomonkey)\
**Post date:** [18 January 2025 03:36 UTC](https://discourse.joplinapp.org/t/notes-and-notebooks-disappeared/43168/5 "2025-01-18T03:36:31Z")

</div>

I tried making a new profile and using the AppImage, but this restored only earlier files that I don't really care about and hadn't actually seen in nearly a year because they weren't visible despite having all the same settings as my previous setup. (same directory, same master password, same encryption keys) My most recent notes are still missing.

---

<div class="post-metadata">

**Author:** ![personalizedrefriger](https://yyz2.discourse-cdn.com/flex028/user_avatar/discourse.joplinapp.org/personalizedrefriger/32/13210_2.png) [@personalizedrefriger](https://discourse.joplinapp.org/u/personalizedrefriger)\
**Post date:** [18 January 2025 04:28 UTC](https://discourse.joplinapp.org/t/notes-and-notebooks-disappeared/43168/6 "2025-01-18T04:28:38Z")

</div>

It may be possible to restore the recently deleted items by extracting printable strings from Joplin's database:

> **From a terminal**
>
> 1. In the original Flatpak Joplin profile, click "help", then "open profile directory".
> 2. Locate the `database.sqlite` file.
> 3. Copy `database.sqlite` to a safe place.
> 4. Open a terminal and run `strings database.sqlite` to log all printable characters to the terminal.
> - This output may contain the content of recently deleted notes.
> - See [StackOverflow: SQLite: undeleting accidentally deleted records](https://stackoverflow.com/questions/454942/how-do-i-undelete-accidentally-deleted-records).
> - The SQLite [database recovery tool](https://www.sqlite.org/recovery.html) may also have the ability to restore recently deleted items using the [`--lost-and-found` option](https://www.sqlite.org/recovery.html#recovery_using_the_recover_command_in_the_cli).

**Using a text editor** :

1. In the original Flatpak Joplin profile, click "help", then "open profile directory".  

2. Locate the `database.sqlite` file.  

3. Copy `database.sqlite` to a safe place.

4. Open the copy in a text editor (e.g. VSCode).  

5. Search for the content of the lost notes.

---

<div class="post-metadata">

**Author:** ![laurent](https://avatars.discourse-cdn.com/v4/letter/l/ce7236/32.png) [@laurent](https://discourse.joplinapp.org/u/laurent)\
**Post date:** [18 January 2025 11:08 UTC](https://discourse.joplinapp.org/t/notes-and-notebooks-disappeared/43168/7 "2025-01-18T11:08:08Z")

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Opened an issue here about the disabled Backup plugin:

> <https://github.com/flathub/net.cozic.joplin_desktop/issues/254>
>
> Hello, I'm not sure what was the best way to contact the maintainer of the Jopli…n flatpak package so I thought I would try here.
> 
> The issue is that the package disables the backup plugin in this line:
> 
> https://github.com/flathub/net.cozic.joplin\_desktop/blob/d32e3fd6f31ad039fbdba25e7e6bcf9e023a71b9/net.cozic.joplin\_desktop.yml#L122
> 
> However that backup plugin is an important part of Joplin - unfortunately users who self host sometimes make a mistake in their config and end up deleting all their notes. It's also a great way to recover everything when a disk becomes corrupted or some other issue. We rely on that plugin to help users recover their data in those situations.
> 
> Additionally although we don't develop or support this package, users still come to us for support which take our resources.
> 
> So I would like to know:
> 
> \- It is possible to enable the Backup plugin (and additionally any other plugin we bundle by default)?
> 
> \- If not, is it possible to put a warning at the top of the description saying the following? 1. We don't support this plugin - do not ask us for help if there is an issue 2. It can be unsafe to use as there is no built-in backup
> 
> Please let me know what could be done. We're happy to provide some assistance and information on how the app should be built if that can help.

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<div class="post-metadata">

**Author:** ![mrjo118](https://yyz2.discourse-cdn.com/flex028/user_avatar/discourse.joplinapp.org/mrjo118/32/23404_2.png) [@mrjo118](https://discourse.joplinapp.org/u/mrjo118)\
**Post date:** [20 January 2025 16:09 UTC](https://discourse.joplinapp.org/t/notes-and-notebooks-disappeared/43168/8 "2025-01-20T16:09:33Z")

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@entomonkey Do you happen to still have the deletion log you exported after the issue occured? If you do, would you be able to zip it and post it here?

When you mention that you don't use any cloud services, are you saying that you use file system sync in Joplin, but sync the destination directory with some cloud provider, or you don't sync your Joplin data to the cloud at all?

Also, would you mind sharing the original destination path you used for the file system sync? I just want to rule out if it's possible that some program or the OS itself may have removed some files from the target directory that Joplin syncs to, which the path could clarify.

My assumption was that other reports of notes disappearing in Joplin were due to something happening to the files on the sync target, but I'm not so sure that's the case now...

EDIT: Actually just noticed the explanation from @personalizedrefriger . Yes it could make sense being a lost permission issue, particularly because on Linux you won't necessarily get an error if ls'ing a dir without full permission, yet you might not be able to see all the files

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<div class="post-metadata">

**Author:** ![system](https://canada1.discourse-cdn.com/flex028/uploads/cozic/original/3X/1/c/1c948e33314e232a0927789508474d8624f4270b.png) [@system](https://discourse.joplinapp.org/u/system)\
**Post date:** [19 February 2025 16:10 UTC](https://discourse.joplinapp.org/t/notes-and-notebooks-disappeared/43168/9 "2025-02-19T16:10:19Z")

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Closed on 19 February 2025 16:10 UTC

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