Hi Van. That's certainly a "bummer".
However, it's possible that this could have a rational explanation, as there's a form of swarming which one never reads about these days, which Dzierzon called 'Pauper Swarming'.
Pauper Swarming - as the name suggests - occurs when conditions within a beehive become so impoverished, so reduced in quality, that the colony considers that moving to another location - regardless of the risks involved - presents as being a better strategy to adopt than staying put and hoping for the best. Essentially, they consider that they have nothing left to lose by taking a chance, no matter how slim.
When seen from their point-of-view, they have been brooding-up for a while now in order to produce 'winter bees', and have been investing significant resources in the process - yet many, if not all of those bees have had to be dumped due to their imperfections. Now of course the bees don't know why things have been going so wrong - they just know that they have, and that the colony is presently in trouble.
Now when most colonies begin dwindling like this, they are caught between a rock and a hard place. They may know well-enough that the colony is in decline, but can do nothing whatsoever about it. So they are forced to stay put, with inevitable consequences.
Your colony however had two key advantages: as they have left some stores behind, this suggests that they had plenty to draw upon when the decision to swarm was made; secondly - and perhaps even more importantly - you mention that temperatures were in the 80's during the last few days.
If you put these three events together: life in the hive being far from good; plenty of stores; and a good-weather window - conditions must then have presented themselves to the colony as being ideal for risking 'a jail-break'. Bees are one of nature's finest opportunists - and great survivors - but only providing that the right conditions present themselves ...
So - the answer could well be as simple as the above. They left, because it seemed the best strategy under existing circumstances. You found few varroa in the remaining capped cells presumably because you zapped their parents back in September - that would make sense.
No guarantee that this is the explanation of course, but it fits the evidence.
'best,
LJ