I had a few sked changes to itineraries over the weekend. Accepted them all, but one is not sticking. It's on a complex itinerary where a very helpful phone agent helped me to apply one RPU to two flights HNL-SFO and SFO-JFK. Even though we're overnighting at SFO, he claimed that the cnx time (about 14 hours) was within the window to count this as a connection, hence one RPU doing double duty.

The upgrade from HNL is confirmed, but I'm on waitlist for the p.s. flight SFO-JFK. Could this be why my sked change acceptance isn't sticking?

I'm concerned about phoning in to accept the change, and having some less sympathetic agent pull my waitlist for the p.s. flight after concluding that I'm over-entitled to use an RPU for two flight segments in this way.

Thoughts?