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I recently inspected a hive that had a deep on the bottom followed by two mediums. On inspection I found a nice brood nest in the top box. The other two boxes were just drawn out comb with some nectar with plenty of room to lay. I moved the top box down one to the middle instead of to the bottom, thinking I would like to keep the deep on the bottom. Now I am second guessing myself. Do I need to go back in and move the brood nest box to the bottom? Or is it okay to keep it in the middle?

You should be fine for now. The important thing is that you gave the queen room above her to lay in. You can decide later if you want to move the deep above the mediums temporarily.