Even if I add the copy that calibre has forgotten about I have to hand edit some entries. Tags that came with books that I delete pop back up. I don't know why. I don't want to automatic merge because I can miss books that way. It's tedious but I want to make sure every book is replaced.
One issue I have with the merge is that it won't delete tags from later selected books. I assume it was designed that way, but that's a big part of what I'm trying to accomplish.
A way to change the M shortcut to keep all the books would be helpful. That seems like it would be the most common use—to merge books in different formats without losing any of the books.