I appreciate all the comments. It's just a mystery with no agent or supervisor able to give an explanation that seems reasonable. It's a SFO-BOS plane that has 4 rows in Polaris and then starts with E+ as row 7 through 12 with 20 and 21 being the exit row. According to seatguru, there are no other configurations of the 757-200 that are similar where an equipment swap would have deleted seats except for the PS config with 7 rows of PS and then starting with row 20 in E+. If a plane swap did occur, it should have been the exact same configuration with the swap occurring within the last couple of day (the last time I checked).
One thing I found out when speaking to an agent the first time about this was that my son's profile didn't show he had a subscription, but when they tried to choose a E+ middle seat (all that was available) they saw it said no charge. So it sounds like there is some issue with their system of not having an E+ subscription always in a traveler's profile and only checks when selecting a seat.