I use the three-deep method of building queen cells. The basis of the system is a queen-right colony that has two deep boxes at the bottom, and then an excluder and a third deep on top. This works well for building because the hive is constantly under the influence of swarm impulse, but it also means that beekeeper has to find the cells that they build IN ADDITION to the cells that were grafted. Normally I find them without any problem by going through the builder every week to remove the cells.
And yes, you have to check every frame, including those honey frames on the outside of the box.
A few weeks ago they built a cell on the side of a frame. It nestled into a depression in the comb. With all the bees, I never saw it. Then I came back and found a massacred rack of cells:
Then I discovered the chewed-out flap of the emerged queen cell, and the killer virgin that caused all the destruction. She came out of her secret cell and proceeded to dispatch all the cells on the rack.
In this case, I had more cells in development but it’s always sad to lose any queens this way. Lessons in vigilance and careful timing never seem to stop in the beekeeper’s world.