As soon as I upgrade a backpack to tier 1 and save/exit the game with it on my back, it has disappeared once I reload the game. I've disabled all other mods now except mod manager and west point expansion. It only happens when the bag is upgraded. The only thing I can think of is when starting the world all three AuthenticZ variants were enabled which maybe caused corruption?
I'm about to try starting a new world with only mod manager and west point expansion enabled to see if the issue is still there - although it will take a while to get to the point of being able to upgrade a backpack.