We had an interesting fight going where one U-Wing and a rebel trooper landed on Ord Mantel under Chirrut Imwe command. The Empire had a tie fighter in space, and a stormtrooper and a shield bunker on the planet. He brought-in Darth Vador for this fight, then I played Chirrut Imwe action card to remove two points of unit in the system, effectively killing the tie fighter and the stormtrooper before the start of the fight, and leaving the shield bunker by himself.

During the first tactical card step, I played Confrontation, and he played Armored Position.

Shield bunker not being able to do any damage, we assumed it was the same situation as a rebel transport during a space battle, i.e. it would be destroyed at the end of the retreat space.

#1 Is it the right assumption, or should we have run multiple combat rounds until all three red damages were done to the bunker?

#2 if our assumption of handling shield bunker like a transport was right, is that loss still a win for the Confrontation card, sealing the fate of Darth Vador?

We ended deciding on a compromise where #1 was true and #2 false, but we are not sure if we messed up here...

Its closer to item #2. Check out the rules for Destroying and Moving Structures in the rulebook for RotE. Transports are oddly destroyed during the retreat step while it appears that structures are destroyed during the next step, (aka Next Round).

I just realized this is a different take on it from the original rules rulebook, structures can stay around a turn longer under the RotE rules.

In the rules rulebook, structures are destroyed during combat if there are no rebel units, rebel structures are there and imperial ground units are in system during step IV (Next Round) of the combat round. Under the new rules it stays around until there is a turn that the player with the structure does not roll any dice, so potentially one turn more (plus that means your Golan Turret doesn't pop just because).

So to sum up, Structures are treated differently from Transports both in what step they are destroyed and structures can hang around a turn longer as well, while transports immediately pop if they have no escort.

In the specific example above, you would play one round of ground combat. I do think Confrontation is legal here.