I find it is helpful to have a (more or less correct) mental model of what is going on behind the scenes with DRM-protected MOBI ebooks. The PID is encoded into the copy of the ebook that you download from your ebook retailer, the MOBI Reader on the V3 "knows" its own PID and so can decode the ebook. Each ebook can have up to 4 PIDs inside, and so can be read on up to 4 devices (the number of PIDs allowed varies from store to store, but is never more than 4).
I find it easiest to manage PIDs manually - go to the ebook sellers site and under "my account" (or whatever) find where to add new PIDs and add the V3. Then redownload the ebooks. The ebook needs to be redownloaded because now it has the V3 PID inside.
It is probably possible to automate this process via Windows Desktop MobiPocket Reader, but I don't know the details of how to do this.
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