I have a problem where my nice model is having a critical feature curiously breaking.

It's an up-to-surface cut, about half way through my tree, and the resulting geometry drives a bunch of other parts through multibody modelling. Now everything is sitting there all stable and fine, but if I go and delete any of the latest modifications at the bottom of my tree (some fifty features down and completely unrelated to the surface-cut (or so I thought)) this one particular up-to-surface cut decides it can't cut anymore because "operation failed due to geometrical condition".

This is absolutely shitting on my productivity. Does anyone have a suggestion about what I could do to remedy such an issue?