I have noticed similar problems due to the co-op characters stored with a party. They can lead to strange apparent inventory disappearances. I haven't figured out the exact failure mechanism. There is some strange interaction happening with the stored co-op character and the rest of the party. This problem also shows up in the inverse. When you're playing co-op, the inventories of the rest of the (regular play) characters stored in the same party save slot don't count towards the item count roundel or the "New" star icon. @DunDunDun, your checklist includes the item "Checking loadouts". Does this include checking the inventory of every character in the inactive/reserve list to the left of the brown party builder clipboard? Your missing items should be on one of them. Also, was the blank loadout you switched to one with no co-op-characters in it? That is, with just one to three regular character portraits showing in the stored party list but the rightmost (co-op) character portrait blank? If it wasn't it might be no good for inventory checking as it could lead to the problems described above.