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OK, I didn't do exactly what you suggested to find out the answer but...
1) was never going to be an option. I knew I was being dumb.
In order to address 2) and 3), I ran insert/replace cover on a book and, hey presto, it now has a replaceable cover.
I've really got noob syndrome and I am very sorry. I don't usually behave like this.
I just don't know what I did to so many books in order to "subsequently edited the epub using Tweak ePub/Sigil and managed to trash the things calibre uses to identify the cover". I'm going to run insert/replace cover on the whole lot, I think.
Sorry to clog up the thread and waste your time. Will you forgive me?
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