You should seek another professional opinion: go see another doctor.
In regards to losing all your muscle ... there is no excuse for not working out other body parts. When I injured my body in a "similar place" in which you describe, I went on a "squat everyday" routine; I got stronger, and bigger. I know this injury can kill your motivation, but you must seek other workout goals and objective. Squats have the benefit of working out your biggest muscles and your core. Be careful with your grip, you will feel the pain in your shoulder if your grip is not good and you position your bar too high or too low (and hence use your arms to support the bar.) If you do squats with perfect technique, you will not even feel the pain in your shoulders.
Depending on what your injury actually is (this is why I encourage you to seek another doctor's professional opinion, you need to know what you are dealing with), you will be given a different advise on how to deal and fix it. In my experience (not a doctor), as with most physical therapy, you need to let it rest and yes it will take months/years to go away if it ever does. The one thing that happens is that scar tissue build up during the slow healing, and in many cases this is where the pain is coming from, after the tendon is recovered; the way to deal with the scar tissue is to work out with very low weight and high reps, slowly, increasing the weight very slowly week after week. Regardless I a not a doctor, DO NOT take this as medical advise, go see a professional.
In regards to losing all your muscle ... there is no excuse for not working out other body parts. When I injured my body in a "similar place" in which you describe, I went on a "squat everyday" routine; I got stronger, and bigger. I know this injury can kill your motivation, but you must seek other workout goals and objective. Squats have the benefit of working out your biggest muscles and your core. Be careful with your grip, you will feel the pain in your shoulder if your grip is not good and you position your bar too high or too low (and hence use your arms to support the bar.) If you do squats with perfect technique, you will not even feel the pain in your shoulders.
Depending on what your injury actually is (this is why I encourage you to seek another doctor's professional opinion, you need to know what you are dealing with), you will be given a different advise on how to deal and fix it. In my experience (not a doctor), as with most physical therapy, you need to let it rest and yes it will take months/years to go away if it ever does. The one thing that happens is that scar tissue build up during the slow healing, and in many cases this is where the pain is coming from, after the tendon is recovered; the way to deal with the scar tissue is to work out with very low weight and high reps, slowly, increasing the weight very slowly week after week. Regardless I a not a doctor, DO NOT take this as medical advise, go see a professional.
"A human being should be able to change a diaper, plan an invasion, butcher a hog, conn a ship, design a building, write a sonnet, balance accounts, build a wall, set a bone, comfort the dying, take orders, give orders, cooperate, act alone, solve equations, analyze a new problem, pitch manure, program a computer, cook a tasty meal, fight efficiently, die gallantly. Specialization is for insects."
— Robert Heinlein