Calrow, over the years I tried several methods of trying to catch the queen if I thought she would be of some value in adding new genetics to my apiary. The one solution that I came up with is somewhat of timing and a daily check on the hive being trapped.
When the number of bees exiting the cone becomes very few and with no new pollen or nector comming in she will be ready to take the remaining few bees and leave. Then I take a piece of metal queen excluder and place it about 2 inches from the end of the cone, then I check it ever day or so until she exits. In the past I have had great success using this method. When she comes out take another larger piece of queen excluder and place behind her and then you can take down your funnel and queen all at the same time.
Like I said it works for me, but maybe too time intensive for others. AHHH! Ain't it wonderful having all this time on your hands to play with the bees!