I don't think you will be a happy camper. When you change the folder for CC it moves all the books in the older folder to the new folder. I don't think that is what you want. Instead you seem to want separate CC databases that show only books in a particular folder (or somewhere), which isn't what CC does. There is one database describing all the books that it knows about on the device.
If you are willing to mix the books together in CC but want to know which library the books came from then you could do that with a custom column duplicated across all the libraries that contains the library name. You could then group on that column to see only the books from one library. A library-name tag could also work.
If you really want to see only books from one library then CC isn't going to work for you.
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