I bought an M fare BOS-EWR-FLL a few weeks ago. PN=0, so no instant clear. I've been watching daily. This morning (still a week out), I saw that PN=0 on BOS-EWR, but PN=2 on EWR-FLL, yet, no automatic clearance. I logged into the reservation on the app, and for the BOS-EWR it still said, "CPU Eligible." But for EWR-FLL, it said something to the effect that upgrade space was now available, and to "click here" if I wanted to confirm an upgrade. It went through right away, and PN decremented to 1.

The lesson is that outside of the CPU window, one must monitor and grab the upgrade when PN (or PZ) becomes available.