The squat is a complex movement. Moreso than the deadlift. So when you don't do it for a while your body sort of "forgets" how to do it well. There's a lot more to it than that, but that's what it means for you. Now that your knee feels good to go, just get back to it. Your body will relearn the movement and your strength will come back in no time.
Don't get discouraged. It happens to us all at one point or another. About 2 years ago I was squatting about 315, then one morning I got out of bed and my left knee wouldn't bend. It just wouldn't bend, and if I tried to make it bend it would hurt like hell. It was months before I could squat again, and when I did I had to start with the bar. 135lb seemed impossible. Funny to think about, considering where I am now.
Current PRs at 242- 495, 345, 585, 1425