Hi, thanks for getting back. I eventually found a kind of workaround. On another forum somewhere (I don’t remember) I read that a person had several layers on his terrain for roads, ocean, etc. He discovered that by toggling the “Eye” of one of his layers, it kind of resets the tool to working properly.
For me as I was working, anytime it started acting incorrectly, I would toggle off my roads layer, watch the topology change, and then turn it back on, wait for the topology to return, and then The flatten tool worked as expected.
I hope this gets you back to your game.
Cheers!