Interacting with Terrain Objects (Trees, grass, etc)

I am working on some scenes in which i need the player to be able to 'destroy' a tree, grass, etc etc (paintable terrain objects), and have it be saved that they destroyed it.
The scene itself is used more as a 'template' for a level. So I assume the process would go something like:

[Player Loads level]-> [Player destroys trees]->[Game stores information of which trees were destroyed (serialize)]->[Player exits level, and returns (scene change/reload)]->[Scene checks for which objects have been destroyed, and does not generate them on scene load (effectively removing them from that 'save' of the game)].


I believe i have found a bit about how to remove them from the scene at run time, but those changes only stay effective while the scene is loaded. Once the scene is closed, and re-loaded, the terrain just regenerates normally (as it should).

What is the right/efficient way to tell the terrain which tree's in the scene to load, and which not to load?

Thanks


Sidenote: I'm new to unity (have only dabbled in a few things here and there). Sorry if this is a blatantly stupid question.