I have Psoriatic Arthritis which has degraded my Achilles tendon to Heel connection. I'm not sure if your condition is autoimmune related, but it may be worth looking in to
(talk to a rhematologist- it took me several years to figure out what was actually going on w/ my Achilles). I take methotraxate and embrel weekly which allows me to actually walk. The above cocktail slows my immune system down and reduces the TNF produced that are attacking my joints/ tendon insertions and causing inflamation.
My injury is trauma related (rugby BITD). It does not affect my everyday life. Yet after hard sustained pitches, especially slaba and stemming corners my achilles feels as though it will blow out. This is something the doc told me could happen.
I have heard that it is hereditary, though the family is without this affliction.
I think I may carve a hole out of the back of the shoe, line it with some mole -skin and give it a go.
What I use to have people do with their running shoes is cut a "t" through the heel counter. Mark the highest point of the bump. That is where the two lines of the t cross. Cut an inch in each direction. This can be tough if the shoe has a plastic heel counter. I have tried this with approx. 10 people and it has worked every time. Good luck.