This is very helpful, thank you, I think I've found the root of the problem (it also explains why I never ran into it before, I don't tend to swap weapons while on location so I never thought to test it). When a weapon is equipped, it saves its "location" as the entity ID of the person that has it equipped. The issue is that it wasn't updating this information of the clip item contained inside the weapon, so it was still remembering its location ID to be the NPC that originally dropped it, who isn't persisted in the save file so it ends up as a dead reference. I should be able to have a fixed version up later today.
The fix won't be able to do anything related to issues already in your save file but it will prevent it from re-occurring in the future.