I guess I agree with the others that you should keep squatting. Barring that, walk more up hills and mountains. Walking fixes a lot of things.
The reason I say keep squatting or walking is that last July something went out of whack in me. I just didn't feel right. It was so vague and it didn't seem to go away. I could still squat okay and hike okay, even backpack, but I just didn't feel straight or right or something. One day, after having spent several sleepless nights with a lot of pain in my lower back and butt region, I was leaning forward at the dinner table and felt this pop in my back. It was enough that I went "oof". After that I have felt straight and right again. Also, I do not like to take pain medication but I did take ibuprofen to help me sleep right before this happened. Perhaps that also helped.
My problem was all in my back and butt while yours is in your knees so you aren't going to have the same experience. But I think you should just keep using your knees. Maybe not squats, maybe something else, but keep putting some kind of stimulus on them and on the regions that connect to your knees, basically everything in your posterior chain. Make this stimulus something that forces the issue somewhat gently. Perhaps whatever is out of whack will move back to where it should be.
Female, 5'3", 49, Starting weight: 163lbs. Current weight: 135 (more or less).
Starting squat: 45lbs. Current squat: 180 x 2. Current Deadlift: 230 x 2