That is not a hole related bug. It is just the selection bug or smth, I do not even have an idea how to fix it.
Really a lovely release. But I'm still standing here waiting for scalable textures, that's something I would really love to see done in Noggit.
Don't delete any files. Noggit _HAS_ to save adts around the modified one, otherwise it won't work.
I know the duplication bug is solved by saving all the adts around the one you change