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@iostrym: Yes, I do this all the time. I have to main calibre libraries that should have no books in common. The collections work fine for these. But I use several others for testing. These get copies of books from the other libraries plus books from other places. Again it works correctly. The issue you will have is that the collection management will be done for the current library. That means that if in one library should be in a collection, but the other library puts it in a different library, then whichever was the last you used will be the one that sets the collections for that book.
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