The usual thing i do to remove things from save follows:

>make a back-up copy of the savefile from the savefolder by copy-pasting it in another folder (i.e. desktop, documents, literally anywhere in your computer):
>make sure that all in-game items related to the mod must be removed (destroyed, deconstructed and the likes) and then quit to menu
>go to mods option then remove the mod from the current mod list, restart the game then load the save file; if it works, nothing will be changed.
>if it doesnt work and breaks the game,1)close the game 2)Delete the broken savefile 3)paste the back-up copy 4)start the game 5) load the backup save file