So just to be clear, your config is: top box - medium - full capped honey; middle box - deep - full capped honey; bottom box - deep - 2 frames brood and rest capped honey?
btw that is very unusual, and cannot be determined by peering from top of frames into box - bees can have top inch full of capped honey, or whole frame - looks the same to us peering above. Peering in from below the box is more informative, if you prefer to peer instead of pulling frames.
The bees can actually die if they have no open cells (or too few) to have the "heater bees" go into to generate heat for the cluster. The bees that contract their wing muscles in the cluster apparently need to be in the comb somehow. So, it is possible to feed too much - for a queenless hive. For a queenright hive, it is not possible, as there would be brood occupying cells (can't put syrup/honey there) and there would be "pressure" from the laying queen that cells need to be kept open for her to lay. They would instead stop
You want the bottom deep to have 8 frames free of honey. It will be quite intrusive to "make this happen" by removing full frames from that bottom box, which increases the chance you lose or damage your queen. Two options come to mind:
1) Are you really really sure there are only 2 frames with brood in the bottom box, and the rest of the box is capped honey? If you are, that is waaaaaay too thorough of an inspection this time of year - next year, remember you have to weigh every inspection with the chance you'll kill the queen. I aim to take out 3 frames tops from a box, since the other side of the box is a mirror reflection - so frames 1-3 are identical in "use" to frames 8-10; if 1-3 are all honey, 8-10 will be too; if 3 has capped brood, then brood will extend all the way to 8. So no need to pull frames on "the other side".
1A) By "are you really sure", I mean, did you pull more than one frame down there? The tops of the frames may all have honey - probably in the bottom-most box that is the top inch for frames 3-8.
If you did not pull each frame in the bottom box (which is good - don't do that now), then I would bet you are unaware that they are fine.
In a couple weeks, their popuation may be down by half... it's part of their life cycle. But with this many bees now, they will benefit from all that honey later. Though the top medium is overkill if you know there are at least 8 frames of honey in the top deep (middle box).
2) If you did pull enough frames in the bottom box to be sure that only 2 have brood and the rest are capped honey, one option is to EXTRACT HONEY from 6 frames from the middle deep. So, completely remove the middle deep, first by taking it off, then putting it above the medium, and then either using a triangle escape board, or perhaps just taking out 6 capped frames and replacing with 6 frames that are undrawn. I avoid leaving empty space for long, but you could for a day if you 1) can't remove all the bees from the deep, and 2) don't have undrawn frames, and 3) can get the extracted frames back to the hive in a day or so.
THEN... drumroll please... to avoid removing frames from the likely queen-containing box, place the deep with the 6 extracted frames (center them) ON THE BOTTOM of the pile. Now the bees have plenty of room to cluster, and with the medium at the very top of the stack, they have plenty of honey no matter what.
Oh, have you "hefted" the bottom deep? If it is full of honey, it will be 70+ lbs - you will struggle to heft it, and it may be a similar weight to the top deep (which should be full of honey and totally heavy). If it is noticeably lighter, then you're fine, and things are "working" fine.
One weird tip for next year: if you get into late April and the top medium is still all honey, and the middle deep has more than 4 frames of honey, it is possible to have too much honey. Next year, it is the reverse problem - you want maximal space to store nectar in the second week of May through JUne, as in they will bring in possibly 2 medium boxes of nectar a week. That gets dehydrated down to half box or so of honey in a week, so I'm not saying you will get 2 boxes of honey in a week.
nectar is 25% sugar and honey is 80% sugar, and with math, we know the bees need extra space to store nectar then can condense it down to honey. You will definitely want 4 frames of honey in the top deep (middle box), but NO honey in the medium, so they can't backfill the brood nest and block the queen from laying and instead prompt the hive to swarm early.