Re: Clipped/marked queens?
If it's done properly it has no effect. However it is easy to damage a queen, even a bit too much pressure on the abdomen can mean she will dissapear from the hive a few weeks later.
How it's done and how much handling varies from one breeder to another, although for these guys time = money so they are usually pretty efficient and get it done with surprisingly little handling. Some breeders will pick up a queen by the thorax, me, I just hold them by the wings. That's just how I was trained, not sure if there is a right or wrong way. I hold them by the legs for marking.
Like all jobs there is skill involved however a person can learn marking and caging queens fairly quickly. But people vary, some people are just naturally good, and others are just naturally rough and will never be good queen handlers.
Oldbee sounds like you've had some poor queens. Even the best queen breeder can do a few poor ones because something can happen during mating or whatever and it's not really known till after the queen has been laying a few months. However if you've had more than your share, vote with your feet, don't buy from that breeder again.
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