If the Beetles take over they will rapidly infest all of the comb and remaining brood, so at that point all is lost with the tree colony. What to do with the bees in the bait hive is up to you...give them a queen by however means or combine with an existing hive. Remember that the bees in the bait hive are older bees and will decline in population pretty quickly once you take them away so unless you have the resources to give them a queen it's best to combine. If you keep a close eye on the trap out you'll notice a point in which virtually no bees are exiting the tree. That's when I take mine away...before the SHB gets a foothold.
I don't know if this would be the right way for you or not. I'd love to be able to let the trapped bees rob the tree out, just don't think it would work here.
Best of luck to you! Keep us posted on how it goes.
Scott