To start off, I don't mean like in Knights of the Nine, with a Knight of the Divines fighting an Ayelid with an alignment to the Daedra, I mean if the actual Gods and Daedra warred with each other in space (or wherever the hell they are), and their physical forms (plane(t)s) at physical risk of death and/or destruction.

So... What would happen? Would Nirn (and any other planes of existence) be wiped out? Or just abandoned?

I figure it would be like something from Raymond Feist's Riftwar Saga, which told of the Gods warring with a race of higher being called the 'Valhura'. The Valhura were incredibly powerful dragonriders, yet mortal. They could coast the streams of time and space, thus could war with the gods (Also mortal in this 'in-between' plane. The Gods numbered nearly as many as the Valhura, which had unverified yet very very high numbers. They used natural disaster, the destruction of worlds and armies of slaves (Valhura created/ used Elves, the Gods created/used Men) to fight. This literally tore apart existence, and humans escaped from their homeland (which was not verified but is known to be Earth) via these portals/wormholes/rips in time and space and populated all of these other worlds.

But who knows? These are two different universes, after all.