Meniscus Flap and Some Jumpers Knee

I have a left knee issue that causes me some pain but generally does not affect my movement. My physical therapist says I have a meniscus flap and some jumpers knee. I also have structural issues due to the leg having been reconstructed 25 years ago (tibia rotated inward). She tells me that I shroud not do squats any more. However, medical professionals are always very conservative in advice. Does anyone have experience with this? Do I have to give up squatting or adjust it (sumo)? What about switching to trapbar lifts? I don’t want to ruin my knee, but I don’t want to stop squatting if not necessary.

I tore my lateral meniscus (along with my ACL and fractured my patella) and was able to successfully perform box squats without pain. The lack of reversal from eccentric to concentric was much easier on the knee, and still allowed me to push pretty heavy all things considered. The prowler is another amazing tool for training the legs while being easy on the knees.