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)
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.
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 includes instructions for restoring from a backup.
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).
Set up file system sync in a different distribution of Joplin (e.g. the AppImage, Snap, deb, or web version), then export to JEX. Next, import the JEX in the Flatpak version of Joplin.
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.
@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