While it takes more time than if two versions of calibre were ran at the same time, you can run a duplicate check, take the list of duplicates and copy it to a text file. Save the books that are in the current open library to a "working look at file" and go to the other library.
You can then go through each book. It takes a bit more time, but the current way the calibre database files are saved means only one instance can run at a time.
I agree it would be very useful to be able to open a second instance but the program is so wonderful we just make do with work arounds.
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