Download SGSC and install it to a useful, accessible location. Most cleaning and diagnostics can be done with this tool, and it is fast and simple to operate.

Save and quit the game (At this point you have a 'clean save') Install updated version of the mod Launch the game and load the save from step 5 You can also consider using save script cleaner on your save from step 5 to make sure your save file doesn't have any records related to the removed file. While the below specifically refers to cleaning saves after removing mods, it pretty much generally applies to cleaning saves in general. The best tool for cleaning a Skyrim save is called Save Game Script Cleaner. Save and quit the game (At this point you have a 'clean save') Install updated version of the mod Launch the game and load the save from step 5 You can also consider using save script cleaner on your save from step 5 to make sure your save file doesn't have any records related to the removed file. Mod description: Prevents saved-game file-size bloating by cleaning the game of actor and item references that are no longer required.

Skyrim save game script cleaner