It appears that there are 2 issues. First, as originally posted, they are not drawing out the medium and second, the brood nest is honey bound. My initial reaction would be to drop the medium between the deeps. They "should" start to draw it out to recover. Once they have started it well, shift the top deep to the bottom. Another option would be to extract some deeps, but that would only solve the 2nd issue and takes a lot of time/effort.
Iddee has a point that we don't know where the honey dome stops. If it is well into the bottom deep that could be a problem.
I've had a couple hives do the same thing this year. My solution is to pull up honey frames, but I'm on all mediums and have that flexibility.
In a related note, I have noticed I have a tendency to give them too much space too fast for fear of swarming. This leads to incomplete and odd drawing of frames in the nest and consequently a lot more work/frustration for me. These seem to be the same hives that won't draw out frames above. But, that doesn't sound like your issue.