Rabbit is suddenly terrified of getting nails clipped

Bugs' nails are very overdue for a trim. I've been trying to clip a foot for weeks. He usually is very cooperative during nail trimmings but is grunting and pulling his foot away right when I'm about to clip down lately. His nails clearly hurt and I need ideas for how to get him to think of nail clippings as fun. I give him a treat always after I try to clip them. Is it possible I taught him he gets what he wants when he bites and grunts at me along with a bonus treat?

Rabbits seem to know exactly where their quick is. If you begin putting pressure on a nail and they jerk away, that means that had you continued clipping that nail, it would have cut the quick. By doing a test pressure on a nail, bunny will let you know if it is too short.

Maybe try doing shorter clips.

As for whether or not you've rewarded him for naughty behavior, that's an interesting thought. Perhaps he should only get the treat if he's behaved well. If he does well with the clip of a single nail -- give him a treat then. (Pulling away on a test pressure is still good behavior, but don't reward unless you are able to adjust and get an actual clip. Wouldn't want to 'train' him to jerk away.)

I will do two clicks them fully clip the nail. He will stay still and not even flinch during the first clicks but pull away when I go to clip. It seems with spring his nails have gotten darker, although that may just be in my head. He has dark nails as it is, but before I could just work out where the quick was and now I can't even see it. I tried a flashlight to see the quick but that blinded me so I had to turn it off.

Maybe do one click, then clip?

If his nail is overgrown, the quick will have grown out as well - to get back to "normal" you need to clip smaller amounts more frequently (every 1-2 weeks).