I have a big hole in the ground beneath the gate leading out from the IC Arboretum to City Isle. I assume that this is due to a conflict between Better Cities and a dirty edit in some other mod. I'm pretty sure that I've used TES4Edit to clean everything that BOSS says should be cleaned (as well as everything that BOSS doesn't know about), so I've probably missed something, but I have no idea what.

Are there any techniques that can be used to figure out what mod reshaped the landscape there other than by running through my load order disabling things until the hole disappears?

(I expect that someone will ask me to post my load order, but first I want to see whether there's a reasonably easy way to determine this for myself before asking others to look for known pairs of conflicting mods.)

I have no idea on this one. My first thought it that you are missing a needed patch, but we won't know without that accursed load-order. It might also help to link a screen-shot of the hole and surrounding area.