First of all, Kovid, thank you very, very much. Your quick and effective help is greatly appreciated.
In the end, "pragma user_version=4;" did the job. Calibre is now working for me again, I have two independent file backups of metadata.db which is now stored in git as well - just to be sure.
Looks like sqlite3's ".dump" does not
dump everything Calibre needs? Is there another way to create a "calibre-compatible" dump?