So say I want to make a boss so big they them selves are the background and I make the enemy invisible so you just see the background. Is there a way I can make the background turn into something else or fade off when the boss is defeated? And also is there a way to change it before the battle ends say if I want the suronding area to become more damaged?
I don't know how to directly change battlebacks mid fight. But you might be able to create a battle event of some kind that fades out the screen and turns on a switch to trigger an auto run event on your map then abort the battle. Have your auto run event change the battleback for you and then restart the fight through that same event - fading back in the screen. That might give you the effect you're looking for with a little bit of tinkering.
As far as making monsters turn invisible - you could just make a new monster with no graphic and transform the monsters you want to turn invisible into that.
Edit#
I forgot to mention this, but I think when you abort battle the screen will revert to how it originally was before the battle started. So you may want to turn the screen black
before the initial encounter begins to make for a smoother transition between the linked fights.