As usual when any news emerges involving a Royal, we now have an outbreak of ignorance, heavily tempered with prejudice on Pprune.
If you are not cap badged AAC, you do your flying training followed by a three year tour as a squadron pilot. You then revert to your own cap badge and do further tours at regimental duty or on a staff. Harry is a captain so he has been given an SO3 staff appointment at HQ London District, one for which he is ideally suited. He may be asked at a later date to return to the AAC for a further flying tour, possibly as a Squadron Commander.
Happened to me and thousands of other Pongo aviators.
What's the problem?