I did it as I said, meaning: I plugged in the old SSD where I had joplin with all my notices, turned off Internet, opened joplin and exported everything in all possible formats, plus the joplin-desktop in configs.
I was able to restore notices. Unfortunately, this is a highly personal solution, so it won't be helpful to others.
Still, I'm disappointed that it even happened. All I did, was to install joplin on another distro and logged in to sync. Details may reveal why it happened, but such basic and normal action should be correct, and if something is about to be deleted anywhere, joplin should stop it, or ensure that this is action we want to do, or if the sync was not complete somehow, it also should inform us, and stop syncing back.
Or, the sync on Dropbox was somehow bugged from the begining and I didn't know, till I synced on another device? At the moment, when I imported my notices, I see:
Created remote items: 356
Downloaded objects: 400
No idea what those 400 objects are, nothing seems to changed on the app side, but it looks like it exported a lot of notices, which is good.
I also learned, I had to create another backup of notices that is not connected to sync, because as it turnes out, sync could be a devastating action.