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I did my first cut out a bit ago. I put most of the brood comb and some honey in new frames and added that to the hive. The queen was on one of the brood pieces when I put it in. A few days later I went back to check on it and no bees at all. Apparently they didn't like their new quarters and just left. Why do they do that?
Lucky for me I've never had a colony abscond. Your case does seem interesting though. Bees rarely abandon brood. Did you investigate the hive for signs of why?
Nice name NCSU! I studied under Dr. Ambrose and Dr. Tarpy at NC State, graduated in '07.
But, to the topic, bees abscond mainly because of stress.
I've had some leave and abandon brood, although mostly from my observation hive. If they don't like their digs, and they are stressed out, it will convince them it's time to go somewhere else.
When doing a cutout, it's usually best to get the queen in a queen catcher, and keep her there for a few days. The bees settle in, and their sent is everywhere. They are less inclined to leave then. I do the same thing with my OH. Whenever I put them in there for the first time, I seal them up for about two days. After that they RARELY are interested in leaving. Too much invested in the current home.