Found it 
It was a timing thing of the NAS: it got an unreachable NTP server configured. And after some reboots it thought it was back in 2001. Most likely its battery died already some years ago. So all new files had a modification date of 2001. That brought Joplin to think 'nah, that old stuff is not synced' ...
Fixed the NTP-server and touched all files, now its back to normal.
Sorry for the fuss 
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