In addition, we are specifying Gen 6 or 7, because any lower Gen Fly Pikachu get's "Fly" removed when transferred.
(HMs moves were removed during transfer, for lower generations)
Have multiple save backups and save states,
then edit the .ini in notepad and change the save format to "Raw".
It may force you to create a new save from scratch, then load up your save state then proceed to save in-game.