This is not new and can happen for multiple reasons

The most common reason is a change of aircraft that cause a "seating sweep", readjusting seating due to the change. In these case, unsupported E+ access / courtesy access E+ will be swept back to E-. It is a flaw in the courtesy system as it is not "supported" access. This is a computer run process that has no information on the courtesy access.

This may have also been a case where a GA notice the anomaly of an unsupported access and needed the space for a supported access E+ passenger. Lack of a PNR comment on why would not help. (if the seats went empty, then probably wasn't this)

This reseating sweep process has been true for as long as I can remember.

If noted in PNR comments or if you call again (although this case was very much out of the norm) it may have been possible to restore if noticed before boarding