I set up the forest maintenance xml and generated it. I deleted the one on my server and put the new one in through FTP. It didn't seem to do anything. Does it just control what grows in the areas once enough trees die to go below the coverage % threshold? I was honestly hoping it would wipe out all trees on my server and replace them with what I set in the xml.

If that's not how it works... is there a way to delete a ton of trees (like 75k-100k) without breaking the server? I found some code on the forums, but people are saying it breaks servers now.

Does it just control what grows in the areas once enough trees die to go below the coverage % threshold?

Yes. It defines the desired state of the forest. The server will move slowly to that state step by step with each midnight cycle when the forest maintenance is triggered.
The problem I see on your server is that you have way too much forest soil. You can work around it by drastically reducing the coverage percentages in the forest maintenance to get a forest that is similar to the original map´s one.

If you want to wipe out your forest population and move faster to the desired state, you can temporarily set the tree Max Age and Death Border to low values (say 20), so the server will kill many trees with each midnight cycle because most of them will be too old. But note that there's an upper limit for how many trees can die in one cycle, so it will probably still take a few days to take noticable effect.

If you use TTmod, you can trigger forest maintenance manually through the RCON console on the livemap to speed it up even more.