I made a simular mistake last year
After a week the bees moved directly above the center five
frames in the lower box and began drawing comb in the frames above them.
I just moved the drawn frames from the upper into the lower box,
taking out the frames in the lower box, which the bees had not
yet begun to build on. Then removed the upper box.
I always make sure the frames go back in without
changing the direction they were drawn.
I put a dot on the end of each frame (with red permenant marker)
on the back end of the frame. That way I never get them mixed up.