I agree that being able to virtually merge/combine multiple separate libraries would be nice. I have two separate libraries. One contains books on my ereader or destined for it (books that need their css and html massaged have a No in the cssFixed column and aren't yet on the ereader). I can connect the ereader and sort by cssFixed and see which ones need to go on it, first taking care to do the copy+delete thing that theducks pointed out and copying to the other library the ones that I've finished reading and deleted from the ereader. So the other library is for books I've read.
I tried using virtual libraries, one for unread and the other for everything, finished and unread, but whenever I started calibre it would start with the everything one which annoyed me. (I think that's what was happening, or whatever it was it was vexing.)
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