With the iPad it USED to be it didn't charge controller when connected (was an android problem), but this is reverse (controller battery dropping, or rather apparently dropping).
The controller is somehow giving incorrect controller battery reading when in use, but when shutdown and restarted is more where it should be ?
I assume your iPad battery is about same as before, so it's just a false readout.
I would try the cable as Thomas suggested, but it would be interesting to see what happens when you fly a 2nd battery and the controller battery shows o% or close, will it just carry on, or will RTH initiate ?
May be worth trying this in a big open flat area to see before tying in the field in more difficult conditions.
Obviously when fitting 2nd battery to bird, it could possibly reset controller, but maybe not if you don't shut the controller down.