I saved the synth in the Covenant quest, went back to Covenant and cleaned the place out. After, I threw all the bodies in a pile across from the gate to the compound (outside the build zone).

Now, every time I go back to Covenant the loot on the bodies of the Covenant NPC's has respawned. The bodies are still in their BVD's but all of their clothing, weapons and other loot are in inventory.

I also constantly have to fight off raiders who spawn in the same area every time I QT, but not sure if that's a bug.