That's really unfortunate. I was never denied either Flagship Check-in or Lounge access myself. AA have been rather kind to me. I was recently disrupted and had to spend the night in NYC. Because I upgraded to F from LAX to JFK, I would have had access to the Chelsea Lounge before my onward CW connection to LHR with BA that same evening. I asked the next evening if I could still have access given the circumstances and was waived in.