Have you continued riding? Suggestions if you have:
- Switch away from clipless and to flat pedals with like five ten bike shoes. There's no substantial speed difference, but clipless keeps your foot locked into exactly the same place all the time, flats let your body move your knee/foot around a little. Sometimes it will fix itself.
- I actually fixed a decade of right knee pain while using clipless by doing barbell squats. I got the form down and one day my knee just stopped hurting. (However I later hurt my leg and hip doing barbell squats, so...not sure about that).
- I'd say see a doctor, but your post says you already did.

While barbell squats fixed my knee issues, I feel a bit absurd that I didn't just switch back to flats when I noticed I was having issues with clipless but no issues with flats. I bought into the whole "bikers wear clipless" mentality, and in retrospect it was pretty dumb to keep doing it when I realized clipless was causing a specific issue for me.

When I hurt my hip (not my knee) as I mentioned, this warmup/flexiblity routine fixed my "pain inside my hip" problem. No idea if it would help with knee pain:
https://www.bodybuilding.com/fun/lim...ever-need.html

One other suggestion...I also took up swimming. It takes the weight off your joints while also using the muscles. Has improved how I feel. Might be worth a shot.