Ugh, so many errors and bugs since I added generation 6. Sorry about that, people. It happens.
In the PBS folder, there's a file named "tm.txt". In it, all attacks taught by TMs, HMs and Move Tutors are listed, along with a list of Pokemon that can learn the attack. Simply locate Fly and add Fletchinder & Talonflame. Pokemon names need to be written in capital letters and separated with a comma only (no empty spaces). There shouldn't be a comma after the name of the last Pokemon on the list.
Sorry for all the inconvenience and have fun :)