It *was* the books in Cloud Collections that fouled things up. AND I tried to update things (delete the duplicate copies, change some collection assignments) at a location where I wasn't connected to wifi. So I probably wasn't being very smart. I think I overloaded its small memory space.
The few test cases I did first were on books not in Collections. They worked fine, so I plowed ahead with the rest, never thinking that the others might behave differently. Meaning, that the others might really need to be deleted before having the title changed. Oh well, live and learn!
And you are right -- Calibre DID go back and change the OS file names, when I changed the file names back to the real book title (removing the prefixes). Wow!! So I'm golden again.