I'm back to squatting after significant time off due to my job and an old football injury flare-up. I seem to have lost range of motion. It's not that I can't bend my knees past 90 degrees, but it's that I have almost no strength in my legs after that point. I'm still quite strong with the overall lift but my legs want to give out at a certain point in the range of motion. Not used to this at all. Used to be able to squat very deep.
Is this something to do with the atrophy of small stabilizing muscles around my knee? Should I continue to squat heavy and just keep trying to push the range of motion until I get it back? Should I go lighter until I get the range back? Anyone else experienced this after an injury or some time off?
Sounds to me like you've simply lost strength in your hamstrings and glutes, which are what pretty much take over once you go deep. My suggestion: squat what you're comfortable squatting deep, but do a couple heavier sets on your slightly shorter range to keep that strength and power. Then, to further strengthen the hams, train them separately as well (which you should be doing anyway!). That's the short of it.
I agree with this post, I will emphasize that I think you need hit your full ROM squat as hard as you can, don't be afraid to lower the weight so that you can do the exercise properly. A lot of people can quarter squat 600 pounds, a lot fewer people can full squat that amount.
If you are having trouble with stability in the hole, box squatting will likely make it worse.
I would imagine it is primarily an issue of conditioning.
It is typically appropriate to divide your training into 3 phases. Conditioning, hypertrophy and strength.
Take some time squatting 3x8 with moderate weight in a progressive fashion.
Bottom half squats, with light weight, would likely be helpful as well. Basically hit the hole, stay tight chest up, drive with the legs (don't let your ass come up) come up to just above parallel and repeat. 3x8. A little bit of rebound is OK.
Honestly, training heavy right now is the worst thing you could do. Back off, take some time to build work capacity/hypertrophy and then worry about progression.
Get the foundation solid before you start adding floors.
If you're experiencing knee issues, I would highly recommend you do some single-leg work.
You might want to take some time to re-groove your movement patterns with lighter weights, and iron out all of your issues. If you can't squat deep, hip mobility may be partly to blame. Also, being weak out of the hole may be due to poor glute recruitment and weak core strength.
My recommendation would be to take a little bit of time to take an honest and accurate assessment of your current physical state and what limits you from being able to squat, and then make a progressive plan to overcome those limiting factors.
Training with poor movement patterns will do nothing but solidify those poor movement patterns and leave you prone to injury. You wouldn't be getting much stronger for a LONG time if you herniated a disc.