A while back, I remember some "best practice" type threads talking about making a clean uninstall procedure for your mods. However, I don't believe that it will be possible to do so with my mod because of the properties I have to set, thereby making certain references persistent in a save. For example, most of the objects in Helgen are set up on enable parent markers, with half being set to opposite of parent. So what that means for me is that I've had to set properties on many of these objects to set scale and move them out of the world so I can put my new stuff in. If you rebuild the town, and then remove my mod, Helgen is left somewhat barren, lol. I've had to manipulate a TON of stuff to make this all work correctly.
So I guess what I'm asking is there a way to make it safe to remove my mod if the player wants to? Or will they just have to understand that once rebuilt, there's no turning back with the new Helgen?
EDIT: Just to be clear, I don't edit any vanilla scripts, spells, lists or anything like that. I only manipulate objects like the burning rubble piles, destroyed houses, shrubbery and so forth.