Hi there, sorry for the late response.
I don’t know if you found a fix already but what I think I did at the time was hide (and maybe lock) the other layers, and had to make sure that I was working on the correct layer when editing.
I think that was “my” solution. ( Solved - Landscape flatten not working correctly - #8 by Perez-PSLusa )
That is a very huge and ambitious project that I have in mind, and I work alone so I left it in standby for now. 3 months now without working on that project, but I’m almost certain that this was the solution.
Check out my maps if you want: pslusacreative