I somehow don't see the seat reservation system as having been migrated to new software etc. with the change to Avanti on Sunday. Even if it was, it would only affect people booking since then. Any pre-booked tickets and associated reservations would have been created under the previous franchise.

Even with these glitches I wouldn't consider flying from MAN to LHR unless I was heading to somewhere really close to LHR, and definitely not if it was the City or the West End or Docklands.