Game Skyrim Forum

If a custom item (armor, weapon, etc.) is added by a mod then removing that mod will delete all instances of that object in the game. If the mod provides locations or containers then those locations and containers will disappear along with everything in them.

When updating a well-designed mod (which includes not deleting anything it had previously added to the game world) there should be no problem with simply replacing the old version with the new one and then continuing to play. (Just make sure you never try to run the game with that mod disabled, even temporarily).

If it's a house added by the mod then yes it and anything inside it would disappear if you remove the mod.

Bethesda developers provided absolutely not support for removing a mod from the game and continuing to play with the same character other than that warning message about possible missing content you get if you try to load a saved game with a mod missing. Don't bypass that warning and keep playing if you value that character.