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I believe Calibre Portable requires portable libraries to at least be inside the "Q:\Calibre Portable". I'm not absolutely sure but I think it may even default to "Q:\Calibre Portable\Calibre Library" every time.
As a work around, you can replace "Q:\Calibre Portable\Calibre Library" with a junction that points to "Q:\My Main Calibre Library".
Alternately, you can DIY your own portable Calibre by creating a copy of the batch file "Q:\Calibre Portable\Calibre\app\resources\calibre-portable.bat" and modifying it. Caveat, I'm not sure if multiple libraries are supported when using the batch file.
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