In order to strip MOBI and eReader DRM you need to use python scripts from the command line, the best place to start to look for these is the darkreverser weblog. In the comments to the the blog you might even find a Windows GUI version for MOBI that is easier to use. Note that for MOBI you need a PID, and often the best source is the PID of your Windows PC running Desktop MobiPocket Reader.
Calibre only deals with DRM-free ebooks. You may want to use it to convert your DRM-free ebooks to an optimal format for the Pocket Pro. Probably ePub or FB2 will be best.
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