If we had run a console command and got our in-game-achievements disabled, or opened the map editor without realize what it would do, is there any console command we can run from LUA-Console to re-enable in-game-achievements? The game already acknowledges the achievements are with mods enabled, so it seems silly that it would disable achievements when we are already playing with a non vanilla game. But regardless they are fun to watch progress, and so am annoyed that they are disabled.

Once your achievements are gone, they are gone. There is nothing, mods can do about that.

This mod doesnt modify the game's console, which cant be done by mods either.

This mod adds a separate input field/window which allows you to execute lua code, almost the same as how /cheat <lua code> does, but without disabling achievements.

If it can work around not "disabling achievements", can the same ability not be used to reset/restart/renable achivements?

No.