The following happened:
-The player was working fine, but I still had to upload 5GB and do the Wendy tags
-So I thought, hey do a complete rebuild offline, so I can check for doubles, run some VBR error checking etc.
-I used my backup for that since I still had the Empeg as backup in case something went seriously wrong.
-I checked and everything seemed fine since it is very hard to hear the anomalies on a lowfi system like a PC
-So, after 4 days of labeling etc. I made a backup-backup, deleted everything on the Empeg, and uploaded everything again

So, what went wrong:
-The VBR checking was too obtrusive, all VBR files are corrupted (thanks to MP3 Tag Studio). I know for sure since I added 20 files in the end after the VBR checking and they are the only one's still ok
-I should have made a copy of the Empeg before + after VBR checking + uploading. Still 4 days of work lost, but what the hack
-Check the quality not only on a PC but also on a good system like the Empeg
-Think before you do. I am really mad I was so stupid

And to make things worse, I convinced my girlfriend to buy a 2 DIN car finally (check the For Sale forum for some details). So, I did not have to sell the Empeg anymore . This totally stupid "file management" sets me back at least a couple of weeks, if not months, don't know whether I am willing to do that.