Thanks cgrunenburg…a few answers:
Databases are in ~/Databases.
I have 70 GB free on the internal drive. I have six databases totalling 15GB. The affected one is 6GB.
Databases are not encrypted.
I understand that Rebuilding doesn’t fix missing files, but having established that they (or copies of them) were actually present, I went ahead to rebuild so that they would stop appearing as missing. I assume that rebuilding is like reindexing so if they are missing they won’t appear after a re-index.
Searching here for “Rebuild” does find some similar events eg this one, although there are differences.