The only safe place to store items are in chests you own.
I set out a bunch of crap in Hod and Sigrid's house, not in containers. Nothing very useful, but that I might use sometime.
I was testing out commands with Faendal, and he killed Stump.

Didn't think he'd accept it.
Edit: Oh God. Then Embry immediately looted Stump, so I chased him down (He started running) and smacked him with my warhammer. Then Faendal left me as a follower and everyone was pissed.
Edit2: Just realized reloading a clean save doesn't turn off ones like god mode. I should load a save from before I did that.
http://gaming.stackexchange.com/questions/37694/do-console-commands-affect-steam-achievementsThis says I didn't screw up my achievements, but still worried. Didn't mean to play my legitimate save with cheats on.