Some heli pilots have found a workaround/exploit where they are able to flare after the hack. I sometimes see pilots dumping flares ~3 seconds after my hack finishes. When this happens, it's usually the same pilot doing it repeatedly (they've figured it out). Possibly related to seat-switching or somehow exiting and rapidly re-entering the vehicle which cancels it.
Before someone responds, note:
1. This is not due to lag, nor the pilot pre-flaring upon hack notification. It's a full 3 or more seconds of before the flares get popped after I've finished the hack. Not long enough for hack to have stopped, and too long to be a result of lag.
2. This is not because I've hacked a passenger or bailed soldier. The hack takes longer to complete, so I know it was the heli which was hacked.