As far as I have learned, flares are always an indicator that the wall is too long, and the flares themself often hurt much more than walking on the sole. They also cause the white lines to get stretched, which is one of the root causes for white line desease. Furthermore, on typical "wilderness" grounds, the sole will always touch the ground and carry weight. Only on concrete or very stony ground will the sole not do this.
My own horse, as an example, was very robust to walking across stones untill an farrier always left the walls too long, and then he began hurting. By keeping the walls very very short, my new farrier (which actually works according to NHC / P. Ramey) and myself managed to get the horse sound enough to walk across the stones without hurting again. I shortened the hooves every 1-2 weeks inbetween the farrier visits, especially the flares. We did not only flatten the walls but actually produced shallows on the sides where the upper part of the hoof wall was pushed up too much. For the toe, which always tends to get too long, my farrier actually ordered me to not stop at the water line but shorten that part of the hoof up to the white line.
It can be that the sole becomes more shallow because at the first moment it is unsued to carrying so much weight, and thus it produces extra-horn to protect itself. After a time, the effect should drop and the extra-horn should go out nearly by itself or with little help by you.
It can also be another effect: Depending on the ground, how soft or how hard it is, the sole bowl will adjust and get more shallow (soft ground) or deeper (hard ground).
Can you post some pictures of the hooves? From front & side when the hoof is on the ground, and a sole picture as well? Then it might be easier to add some more thoughts.