Green and Yellow EDP's will not be providing output as a result of the APU running.... HOWEVER..... If you have the APU running and the apu gen is working as it should then the Yellow system can be pressurised by the electric pump and this in turn will cause the Green system to be pressurised by the PTU (Barking dog in the hold) as if a pressure differential is sensed between G+Y one will pressurise the other. (No fluid transfer takes place)
The above scenario assumes the engines aren't running and G+Y edp's are not giving system pressure.
There may be altitude restrictions for apu use so a descent to this height may be necessary, cant remember...