Did you have a fix on this issue? I have the same problem with it.
Unfortunately no. Looking through the database it seems to me that most content is gone - although I do not understand the size (~ 12 MB), and whether notes can be stored in the blob entry fields.
There has been at least another thread like this before: thread regarding sync errors and data loss in May 2020.
I have to say that these issues with syncing when making a re-install do make me waver whether I should invest into Joplin as a tool. Data integrity is key for a note taking tool.
Perhaps a good feature would be to ask the user whether he would want to finalize a sync (e.g. 300 files are going to be deleted. YES/NO?)
Where and how is note data stored in Joplin? Is there perhaps a spec?
Cheers!