Well, thanks to a new mod dubbed the in-game patcher, it's possible to resolve issues like that simply by wandering up to the location as the Dragonborn and editing the very make-up of the world. See a rock clipping through a house because you've downloaded a couple of works that give the same bit of Whiterun a makeover? The modder behind this in-game patcher is RavenKZP, whose previous projects include some equally advanced stuff. This in-game patcher, originally spotted by TheGamer, is a plugin for Skyrim: Special edition's script extender. There are a bunch of quick YouTube tutorials under the mod page's video tab to help you get started.