Lost my first full swarm in years due to the same . I could not find the queen to clip her.....and of course was working Sunday (National swarm day, 1st warm day after a bout 10 days of cold wet weather) so no inspections for about 10 days. Monday sealed queen cells and reduced bee numbers and no eggs.
However, the top fully capped super was totally empty of bees so was able to remove and harvest. As a new method of clearing bees it's not to be recommended....