Build up tolerance to knee flexion!
I recently worked with a high-level jiu-jitsu client (with @dr.jasonpark), who experienced pain and discomfort when his knee was fully bent. In jiu-jitsu, he experienced this knee discomfort when shooting (when an opponent forcibly pushed his heel towards his butt in guard), and in any deep squat or half kneeling position when on top.
In addition to freeing up some myofascial restrictions and working on his knee joint mobility, the main focus of our treatment sessions was PROGRESSIVELY LOADING HIM INTO END RANGE KNEE FLEXION IN VARYING PLANES OF MOTION. Shown in these clips are just a few of the exercises we did. The key with these exercises that I want to point out is that we worked at every single 'variation' of knee flexion we could. Constantly changing what position the hip (femur) is in or the actual position of the knee (tibia) itself - ie tibial adduction, abduction, eternal rotation, or internal rotation.
TAKE-HOME MESSAGE: Don’t get stuck working your mobility all in one linear fashion. Work through every conceivable angle and variation you can, as movement and life is not all in one plane!