when the next Tes is out there will probably be a book about the Civil war and possibly mention the dragonborn.

which side do you think will win the war.
what side will the dragonborn be on.

they will have to finnish the war somehow but what will it have in the lore

Neither and both.

I think the outcome of the civil war will be one of those things lost to history and that something so big that it makes that point moot will happen fairly quickly, like another Great War. We probably get some story about the "Dragonborn who united Skyrim and the other human nations in their war against the Aldmeri Dominion".

My money is still on them not even mentioning a winner, only that it was resolved.
"I hear Skyrim is still recovering from that horrible civil war."
"Aye, I hear them say there's still debate over who won."

And that would be IT.

Cyrodiil will be such a mess that all we'll know is that someone won and Skyrim was united in its front against the thalmor.