This is not a debate by any means.

I'm currently doing the CW questline on the Stormcloak side. I currently have a large bounty in Haafingar. After I take over that hold and it becomes Stormcloak territory, what happebs to my bounty? Is it wiped clean or will Stormcloak soldiers attempt to arrest me?

It's gone. I've used this to my advantage before. Murder all of Markarth, give it to the Stormcloaks during Season Unending, and the bounty is gone! Even when you take it back and it's in Imperial control again!

It gets wiped clean when any city is taken by either side. So if you got a high bounty in say, Whiterun Hold, When the Stormcloaks take over Whiterun in the quest Battle for Whiterun, any bounties accrued before gets knocked off your head by the change of government.