I do NOT know how you knew you hadn't vacuumed the queen. I would have simply assumed I had her in one of those vacuum boxes. How on earth did you know she was hiding out?
Liz, I wasn't 100% certain we hadn't vacuumed the queen, but as the evening progressed it was evident something was going on in the void space around the last piece of comb, particularly between those three 2 x 4's and the roof sheathing.
From observing bees on my cut outs I've learned to pay close attention to what they're trying to tell me and it became apparent that she was likely still in there somewhere.
It was by observing their actions that I grew confident she was still holed up in there. FYI, when the remaining bees are acting very runny and are spread out all over the place without focus, that is generally a sign that she's not there.
When they move together in a specific direction as an entity, that is usually a sign she is in there, somewhere.
I feel confident she would have come out of hiding and all bees would have been on the last comb section come nightfall but we decided to take a more aggressive approach by smoking them some to see if we could run her out and that was the charm on this one.