At the Synchronization Status page, I get the message “Items that cannot be synchronized”. There are some files could not be uploaded because of “File not found”.
I check the IDs of the files. These files are some images. They were lost because of my mistake or the problem with my WebDAV server month ago.
Anyway, I found the notes with these images and replaced them with new ones. Then I deleted the .md files on my WebDAV server with the IDs. After restarting Joplin and syncing again, these messages at the Synchronization Status page are still there. I want to know how to remove these error messages.
From your post it seems like that you are getting this because you have deleted files outside of Joplin but Joplin still has references to them in its database on your computer. It tries to sync them but they are no longer there.
I am wondering if a fresh sync with your server could help out here. By that I mean:
Backup your notes to a JEX file
If you use E2EE make sure you know / have a copy of the password
QUIT Joplin (File > Quit)
Move or delete your joplin-desktop folder from .config (cannot be more specific with the location as it varies between OSs)
If deleting remember to backup any custom template or css files in the joplin-desktop folder
Start Joplin which should now open as if it were a fresh install
Delete the default notes
Connect to and sync with your cloud server
Hopefully this will end up creating a fresh Joplin db on your system and populate it from your cloud storage with the notes and resources you actually have!
Another solution, more complex, could be to open the local sqllite database and remove the record with issues from the synchronization table and its associated item.
In my case, I had to remove the record with issues from the sync_items table and the resources table.
Example in my case:
delete from sync_items where id = 765
delete from resources where id = '9218498d321645118a2f163d3e40c020' --id of the item associated with the resource with issues in the sync_items
For some reason, the system keeps a reference to something associated with a note that I've already deleted.
It will be necessary to have a SQLite editor and open the file "database.sqlite" located in the folder ..\joplin-desktop.