I'm actually having the exact same issue as stated above, but it happened even earlier. My one storage chest, which held all my 'unique' and 'named' items, such as the tyrant's set, hallorn's blade, and so on, vanished, replaced with three storage chests along the side wall that are unusable.
My mods that I've been using since before and after there being an issue are:
Druid Class
PartyTest2 (Unlocks the party size)
Rest-urrect (bedroll resurrects after combat)
Sim's Day/Night Cycle with Dynamic Weather
Toggle Polymorph Appendages
Totem Duration (increased turn duration to 4)
I never used any of the mods in the OP's list, so none of those are the cause as far as I can tell.
