Are you using the "Great Soil" lot trait? If so, try removing it and see if that helps.
I was having the same problem in my game, and removing the lot trait seems to have fixed it.
I suspect that trait is broken and likely has been for a while, because I dealt with that whole reverting plant issue for months and have always used that lot trait. So, whatever broke it happened a while ago.
It's been an issue for a lot of players but not all, and something like a broken lot trait could certainly explain that.
Anyway, if your lot has that trait, remove it and see if it helps. Seems to have fixed my issue. I haven't played with the trait removed long enough to be 100% sure it was causing the problem, but all signs point to yes so far. Time will tell.
Hopefully it helps.