You don't need two calibre instances. You can create an additional library (handled from the same calibre) and move the books you don't want in your normal library to this new one. In this way, you only have to switch between libraries for changing from one to other .
There is no problem with this situation, I have more than 10 physical libraries (virtual libraries is another matter, that I don't think it's the proper way for the situation you describe).
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