I'm not an expert and I am not 100% sure what the reason would be, i'm sorry, but thought I would mention something that I experienced with my own horse who was quite sunken in his loin/flank sort of area. Maybe it could be a bit of some help?
Earlier this year in august I had a therapist come up to do treatment on my boy (For info of what exactly, here is the website: H.E.C. THERAPY - MAIN
She did quite a lot of therapy on him (he really needed it) and she had mentioned to me that he was quite sunken in his loin/flank area and it actually had some linkage to his sheath. She had told me he was quite tight up on his back, along his spine, in the section where it is his loin and flank area. What she told me is that when a horse is gelded, sometimes scar tissue (it's that or another name, it's late here i'm sorry and i'm having a hard time thinking it's another name, but can't remember :P) that forms in the sheath from being gelded and can sometimes cause some tightness within their sheath. Horses have like, I guess you could call it, like, nerve strands? (i can't think of the correct name or description right now sorry, i'll do my best) that link from his spine and down towards his sheath (and branch to many other places too), and because of the tightness caused by the sheath, it causes tension that can show up in their lions/flank and spine. So even though they show up 'sunken', tense etc up in their back etc, it can actually be caused by something you would never think possible.
So, it is my duty to relieve that pressure by 'stretching' his sheath. As unpleasant it is, I have to actually reach up his sheath (till I can go no further) to 'stretch' his sheath to help relieve that tension. It's not something pleasant, and Rory wasn't too keen on me doing it, although he was very well behaved, he is now not sunken in where he once was. He has loosened up quite incredibly and that was only doing it after one time. It's something I have to do on a regular basis now as he gets tight in his hind end etc very easily.
So the morrel of my little story, is that maybe get a therapist out to see him, see if it could be related to his body maybe tight somewhere, or needing some adjustment for him to fill out in those places correctly?
Cause just from that little thing I can do myself on a regular basis, it has made a huge difference to Rory's improvement, in both his weight gain, muscle development and overall let him relax. :)
I hope you can find out the solution soon, I wish you all the best! :)