There are a lot of factors that could have contributed to strain on the tendon and deterioration, but the bottom line is that it was still over loaded or unbalanced in its loading. Have you tried immobilization to truly remove stress through the tendon? Yes, you will want to move it through range of motion in rehab, but it sounds like it's never gotten the chance to "calm down" and heal in the slow and questionable way that tendons heal.
My personal experience with peroneal tendinopathy was that the tendon was strained because my posterior tib and/or FHL weren't firing well or were too weak. That caused the peroneals and achilles to pick up the load. Single leg balance exercises actually aggravated my peroneals because I was essentially doing the exercises "wrong." I was still relying heavily on the peroneals for stabilization rather than other foot and ankle muscles & tendons...so they stayed irritated. As soon as I cut out the balance work and started focusing on the medial side of my ankle, the peroneals felt much better and the bulging/pulling/instability feeling improved. SO...try stopping the balance exercises for now and focus on strengthening other parts of your ankle. You're young, so while missing a season or even a year or two sounds horrible right now, you really do have plenty of time to let this heal, and it definitely can heal. You may just need more rest than you're willing to admit.
Other voodoo that can't hurt is: hot/cold contrast baths, dry needling, aggressive massage.