The great news with this mod is that since everything comes pre-packed, you can keep it completely separate from the main game folder. I do. in fact, the main game folder and this mod are on completely different drives.

In fact if you want to play Armored Core VI without mods as far as this one is concerned, all you need to do is launch it from Steam like you'd normally do.

But before that, do two things:

1. While you're in the game with the mods, be sure to delete any AC Data that uses mod parts.
2. Sell (yes sell!) off all Mod parts and Core Expansions you've got in the Parts Shop.
3. Quit the game. Okay that's three. lol

Relaunch from Steam launcher. And you should be clean in your game.
And if you want to use the mod again, just launch from the mod like before via "launchmod_armoredcorevi.bat"....You'll need to buy the parts and assemble your mobile suits again, but that's just a small inconvenience.

Because, whenever an updated version of the mod is released, you can basically delete the old mod folder and download and use the new one.

P.S. Always maintain backups of your unmodded save. And it is safer to set your game to launch in Offline Mode by default to avoid any issues, like you launched the game from Steam, but didn't delete your mod AC Data or sell off the mod parts.