I would expect it to be repriced, just like any other reservation that is changed.
That's a pretty big downside, then. I regularly book individual night but back-to-back reservations when my plans aren't fixed, the hotel tries to charge the higher rate across all nights ($120 for all nights, in my example, instead of just two of them), or when using a mix of cash, points and certificates.
On paper, Pay My Way sounds attractive and I think it is for a lot of people (including myself at times) but if re-pricing is going to occur, I don't see any reason not to continue booking individual nights.