or renamed the files on one of the drives, from fid 100 to, say, a0100, etc. This could be done in a shell script, making it a quick fix.

Good point, yes. That should work fine. All the second drive's fids will be orphaned, of course, but you could fix even that by adding fid a0100 to the root playlist (appending to the 100 file and changing the length tag in the 101 file).

Peter