Keep in mind that as soon as you destroy the nest the queen giant bee will start flying away instantly, so be close to the hive the moment it is destroyed. The queen flys at a slow speed, but fast enough for it to have severe consequences as if you lose sight of it for even a second you might lose it completely. After you destroy the hive you can use honey that is definitely dropped from the destroyed beehive to lure it as queen giant bees don't wander like a normal creature and instead fly in a straight line at like a 150 degree angle when they are initially spawned from a destroyed beehive, so use honey to fix its ai and actually make it start descending to the ground then wander like a normal creature.

If you don't have honey, you can also damage it by using something like a tranq arrow which won't kill it and that will also fix its ai. (obviously this will also aggro the regular giant bees)

If instead the queen bee is too far away to lure with honey, then read the first sentence of the tip again, specifically the second clause.