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Hi Terry,
what is your bee suppliers take on this, what was his explanation ?
Good luck
Would be a little sad if the bees were given out to a novice with no instructions.
A new package can be a little nervous, and it is normal that the bulk bees and the queen are not actually from the same colonies. These are still achieving unity and upon installation in the hive should have an entrance reduced to a single beeway for the first few days, and you should NEVER go raking in the brood box for at least 10 days. I have heard some of the 'suspicious heads' say that is because it gives time for the supplier having given you a VQ to sort itself out, but that is generally untrue. It is the standard method to avoid stressing the bees any more than they have been already. Every day earlier than 10 days that you go into the nest area increases the failure rate. Go in in the first three days and it rockets.
The package should also be fed heavily on installation. A big syrup feed, like min.5, better 10 litres, not little bits of syrup.
Early disturbance can cause queen balling and absconding. At three days it is quite possible the queen has only just been released from the cage, possibly why there were still a lot of bees on the cage, as her pheromones were still abundant there. She would not be enlarged for laying yet, still nervous, still very 'flighty'. Most such queens are from mini nucs at source and will probably only have produced their first worker pattern laying.
You might get away with this but there is a serious risk you have gone in too early to investigate. You SHOULD have been given instructions that covered this.