Which ones exactly? I got a few dialogues of her calling my My love in act 3, and even got the ending with her too when I finished the game. I think you get the least bugs if you just straight up destroy the grove with her, and then try to max out her approval in act 2, so you get in to act 3 with a very high approval.
I did exactly what you said. Straight up destroyed the grove, maximised approval in act 2 and act 3. No others romances at all. And got just one new dialogue "mindsharing" in act 2.
Seems like you're just lucky one to not meet these bugs.
People say the easiest way to check flags working correctly is to visit drow twins in act 3. So included them under spoiler because in my case they are not working.
I didn't get these
Oops I forgot why it worked for me, sorry. I did
this. I edited my savegame to fix those flags. After I did this, both the drow twins and the dryad at the circus acknowledged our relation. Maybe this is why I got the Minthara ending? I have to say though, the fix is not perfect, you get the ending yes and she will call you my love sometimes, but when you talk to her yourself, the dialogues are still as if you don't have a romance. It's still better than how the game is without the edits though. I also still didn't get the second video in your spoiler, I did get all the rest.
If you just do those edits to your savegame without ever launching the game again with the commandline tool enabled, the game won't know you have edited stuff. I still got achievements, and never that message you get when you use mods. I think it is pretty safe. Be sure to make an unedited save as well in case something goes wrong.