Seldom do queens fly away except during a swarm. Most new beeks and even some of us oldies
lose a queen in the grass if we do not remember to hold brood frames over the box until we are sure the queen is not there. Another common mistake is to not provide enough space to lift the brood frame and the queen is damaged/killed when she is rolled off the frame.
Smoke is used to mask the queens instructions to the workers. to much smoke and the workers might think there is a fire and start eating the honey stores before they must exit their hive and run for a new home.
Remember with smoke - Less is More I prefer to give the workers a light spray of sugar water to using smoke. If I go down more then one box, I use a very little smoke at the entrance and spray at the top.
I do not smoke the hive before I remove the honey for your use. - Mike