I don't think they particularly keep track of where points come from (or at least don't care), just whether or not you've used you home week priority for a particular resort.
I own 2 HGVC resorts and 3 affiliates. They are all under the same account. My affiliates have weeks that are pre-booked. If I want to use those weeks, I don't do anything. If I'd rather have the points, I cancel the pre-booked reservation and then use the points.
One example of what I've done that makes me think that it doesn't matter what points are used for your home week priority reservation:
I made club reservations for HGVC resort C (which I don't own) using points from HGVC resorts A and B (which I do own), using most of my available points. Months later, I cancelled my pre-booked reservation at affiliate resort D, and used those points to book a home week resort priority reservation at HGVC resort A. It only seemed to matter that I hadn't used my home week resort priority for resort A at that time. It obviously had to use the points from affiliate resort D, as that's all I had left. (I did all this using the on-line system).