Have you tried pointing Calibre towards the location of the library - either using the wizard or the Switch Library option?
I'm not a programmer but I was kind of under the impression that Portable meant it was best for use on a USB stick or Memory card that is getting switched from one computer to another and that's why you open the program by clicking on the calibre-portable.exe rather than a desktop icon. By moving it the way you did you changed the actual directory structure (\program files\ to \program files (x86)\) rather than just the drive letter. I could be wrong though.
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