[Suicide Junkie]

I meant in the case of draining the supplies when you arrived, but then rebuilding more in the meantime without giving them to the ships...

If you have another planet around somewhere, you could transfer all the supplies onto one or a few ships. Just enough to get them to the nearest other planet with supply. then they could fill up there, and carry the extra supplies back to the fleet.

You could also build a dedicates supply tanker, to shuttle supplies up from the core systems of your empire.