I've never seen that issue before - does it happen after doing anything specific? I'm also not clear on what you mean by clips disappearing - as in they are registered to a character's inventory but don't load in the save, or the clip in the gun itself disappears?
I kind of got both. Sometime I would raid a place that loots weapons, steal a gun and immediately assign it to a character, everything would go fine until I go back to the safehouse and I get a message like "clip(0123456) is not found and had to be destroyed", the gun remains loaded until I quit the game and start it back to find the gun empty, I haven't managed to reproduce this with guns I've found but haven't equipped to any character.
For the other instance, it's just that sometimes I would load a game and get a black screen, searching the log told me that it was because of some missing item, and I practically searched everyone's inventory in the save file to find out that some character would have clips in their inventory, but the item itself of the clips has disappeared from the save (and it happens often with .44 clips, although it also happened once with assault rifle clips). It happens mostly whenever the game saves following some safehouse raid.
I first thought it was because I have the bad habit of alt+F4'd the game whenever I do something stupid I didn't meant to that have dire consequences (like opening a door when there's conservatives around), but it happened once when I quitted the game using the "exit" button as intended (I just got the notification that one safehouse was being raided by either CCS or the Intelligence, forgot which but not the police). Plus I don't think I'm stopping the saving process this way considering that it would only save once my squad is back from whatever they've done and the next day starts?
I hope these clarifications helps.
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.