After lowering too much next to the waters edge I got a situation where several tiles were locked at 0 elevation. When including those bottomed out tiles in new flattening orders everything would end up perfectly flat at the lowest level possible (kinda handy for eating a hill, but not working as intended I’m sure). Nothing I could do would raise them back up.
After a while I noticed that in this area there were some floating road textures about where the original ground level would have been. It is hard to capture in a still, but you the textures that look like they’re on the cliff are directly above the selected road.
This situation with the bottom locked tiles existed in the last save file I sent, though only across about 5 tiles running in from the waters edge. Let me know if you want a newer save with the floating roads that have resulted.