Thanks very much CazMar! That really was an Aha
! moment.
I had no idea Calibre was copying the whole file into its own directories. Therefore the tags, etc., do not refer to the original document! One of the scenarios I imagined, for example, was deleting the original file and Calibre telling me "data error: file not found" or something like that.
Then it's a question of principal! Order! I definitely will organize the original files. And after that, I'll have to get around to those heaps of books on the floor too...
Cheers!