After doing a substantial cleanup of duplicate files, moving junk around, moving folders and generally re-logicalizing the entire library, it became clear that Bliss was now hopelessly confused. I needed to go into the .bliss folder and clear out the database that held bliss's knowledge of the library as it was.

This was something of a pain, although what to delete was in the documentation on the bliss web site. It would be nice to have a button (with confirmation of course) that said "Start from scratch." or words to that effect.