Interesting ideas.
The first one I think should just end when either of the zones is taken over. When you've taken over the enemy zone they're attacking from, I don't think they should continue to attack the other zone from it. Also, on the map, if the two zones swap owners, it's likely they'd become detached from their fronts, and that'd trigger the mechanism saying you lose the zones detached from your front. I think it'd become a bit messy.
However, it's an interesting idea to let two zones try to take each other's flags instead of playing just the roles of attacker and defender. As it is now the attackers don't have much to lose, only the defenders, so that seems more fair. Maybe we should try and see how that works, timed like regular battles.
Progressive battles:
I don't think I'm completely sure about this, but I think that'd be better to have in another war region, having both flags and that would make stuff more complicated and I think the flag concept seems more intuitive and probably more fun.