Boeing are clear, if you are using external conditioned air then the pack switches should be off.
We (Engineering/Maintenance) were told that there was a possibility of damaging the external conditioned air compressors with both running. There is a check valve on the external connection, but it is a simple hinged flap on Boeing aircraft. When we started using more external conditioned air for enviromental reasons, we noticed that more and more of these flaps were getting damaged and even detaching (ending up further down the pack outlet duct)
When you restart your APU, do you normally ask for ground clearance? (I guess not). However, you should ask for ground clearance if you start the packs (if you are not sure if ground air is connected). To me, leaving the pack switches on just seems like another hole in the cheese.