Items in Bags vanish, probably related to quests/areas resetting

Zormau

So I finally remembered that I'd wanted to equip Hexxat with the Firetooth Crossbow while in the druid grove. I had put it in Dragomir's Repose, but the container was now empty, as were my gem bag and potion case. I see two possible triggers: Leaving Athkatla for Trademeet or, what I'd done before, doing Neera's second quest ("visit" the order's sanctuary in the city) and completing that part of her storyline. Everything had vanished from it. Now I bet that I could just go to Watcher's Keep and buy it again, seeing as most quests and areas I had previously visited are now reset, but I didn't know that at the time and used the EEKeeper to give myself the most important items back. I have no idea if there is a smart way to correct the quest and area errors, and I fear the worst for De'Arnise Keep (I'm a Fighter, so that sort of matters).
Maybe I'll load an older save and try to replicate the error.