This happened to me today. When I checked my reservation this morning for JFK-SFO (#766) on 10/13 and SFO-JFK on 10/15 my seat assignments, 23D (E+), for both flights were GONE and I was without seat assignments. I called the Premier line to fix this and they really had no explanation....they looked at my profile and said there was recent web activity on my account involving seat changes....total B.S. as I checked my reservation last night and I was still in 23D for both flights. I did request a mileage upgrade for the 10/13 flight, not sure if this may have caused the glitch but probably not.
Totally unacceptable, but not sure what I can do. They re-booked me into 25E on the outbound (really psyched for 6 hrs of middle seat

) as no more E+ aisle seats were available.