How do I use hidden deck fasteners without compromising the integrity of the flashing?
Aluminum flashing can not be in contact with pressure treated wood(it will eat away over time)  I use ice and water shield or a window wrap in between flashing and PT ledger board  this will seal around screw and not leak.
To be honest though the amount of water that will make its way under the clip and through the hole and back towards the house is soo little,if any, it will not do any damage.