I rarely shake bees on site WHEN I have not caged the queen. I have had them abandon brood a few times in the past & have had to oust them out of the new spot as Scott suggests. I also notice as the season wears on & it gets hotter the bees don't seem to cooperate like they normally do earlier in the season. When its really warm out I generally avoid shaking them on site even after the queen is caged. Instead of going right into the set up they will bunch up where the hive was prior. Unless you shake them after dark in pitch darkness.
Thanks for the inside tips, JP.
Those bees did NOT, in fact, reenter the house, thank goodness. All but about 10 of them left the box into which I shook them and they flirted all afternoon and early evening with another spot (far far from where the convenient scaffolding was located) and by dark they were all clustering in a big ball at their new (very high) spot of interest. I climbed a ladder and vacuumed them and took them straight to their new bee yard. The next morning, the contractor caulked every gap he could find.
BTW, JP and schawee and Scott and anyone else who can find the queen during a cut out: I have NO IDEA how you do it.