I know it says in the manual that you are not to store loot in containers that you don't own unless they are in your own house. But had anyone stored any loot in a chest in a cave that they have cleared of all bandits to find that there loot is gone once they return to that cave later in the game. I'm just wondering how safe this is.

Don't do it. It likely will disappear.

Any chest outside of an owned home can respawn, and since we don't really know the rates it could go at any time really.

About 3 ingame days I think it shold be reasonably safe you you traveling back and forth between venders.

theives guild is safe.

so is mage place.

don't know about companions but I would assume so.