To start off I'm a high school senior. About six months ago the area around my ankle started hurting a lot and began to swell. I went to the doctor and was diagnosed with Posterior Tibial Tendinitis/Tendinosis. I had to walk in a boot for two weeks and then take another two weeks off with no activity. After the time off, I did physical therapy for about a month. I was also given custom orthotics.
After the physical therapy, I started slowly running again, adding mileage carefully with my team. Sure enough, the pain started slowly returning but it wasn't nearly as painful. So I decided to keep running. However, the area is still decently swollen but the pain is minimal.
Then, exactly a week ago I was running and my Achilles Tendon began hurting at the end of my run. When I stopped it only hurt a bit, but two hours later it was excruciating. I took some Advil and iced it. It hasn't been hurting too badly while I run, however, afterwards it is very painful.
I went to the doctor today and he told me that I needed to go back into the boot for two weeks and start physical therapy again. My question is if I take off from running and come back when it feels better, what's stopping the injury from just reoccurring? I also have extremely flat feet and a decent leg length discrepancy. Is there anything I can do besides taking more time off and missing the rest of winter track?