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I wouldn't go Sabardeyn's route, because of what BetterRead said: you can make mistakes.
If you create two virtual libraries, everything is still in the same physical library on disk. If one of you makes a mistake, the other could get into problems. Even using two different libraries may not be ideal, as you may not want to have your Calibre set up in the same way.
Going with two installations of Calibre Potable, that each contain everything into their own folder, is actually a great advice.
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