When bees reproduce, their colony splits in half, said Jay Evans, research leader at the Agriculture Department’s Bee Research Laboratory in Beltsville, Md. Half of the colony stays in the hive with a new queen, and the other half swarms with the older queen to a new home.

But in late August, swarms tend to happen because of overcrowding and possibly overheating within hives, Mr. Evans said . So, could the bees simply have been too hot?

Alex Aubry, the executive chef at The Stinger in the lobby of the InterContinental, has beekeeping built into his duties . He said he was initially nervous around the insects in 2016, when he joined the eatery that serves cocktails and food laced with honey from the rooftop hives.

“To be a beekeeper, you have to be certified,” said Mr. Aubry, who now finds the work relaxing. “They teach you how to handle the bees, how to take care of them, what to look for. Making sure that the queen’s not leaving. If the queen leaves, everyone’s gone.”

Mr. Aubry was adamant that the Times Square bees were not from his hives .

“ They were from the Hilton,” he said. “It wasn’t ours. We always check.”

Mr. Aubry then described the maintenance that he and his sous chefs provide, adding that after he heard about the swarm, he and a sous chef quickly determined that their queens were still nestled at the bottom of their respective hives.

Mr. Aubry invited me up on the InterContinental’s green roof and let me borrow a beekeeper suit, so I could see the insects up close. The roof had plenty of space for a large garden of flowers and herbs. The bees buzzed in four wooden enclosures.