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I use a Macbook Pro and have Windows 8.1 running in a virtual machine.
I very often have Calibre running on both sides of that, at the same time.
As long as you don't try to use the same library on both sides at once, everything works fine. Either side can use any available library.
The only other thing to worry about it is just don't "copy" to a library that's in use on the other side.
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