I’m very sorry your rabbit died. It does sound to me though like something was wrong with her. Rabbits can be scared when handled, but we must all handle our rabbits even though they might not like it. We have to clip claws, check for poopy butt, take our buns to the vet etc. Buns may not like any of that and yes, they can hyper-ventilate with fear, but normally they don’t die just like that. A rabbit can have a weak heart, that would make the rabbit less tolerant of even normal stressors, but a healthy rabbit doesn’t just die from being picked up by their human.
I’m thinking there could have been something wrong with her that made her react with such fearfulness towards you. Rabbits hide symptomes of illnesses really, really well. This is so they wont attract the attention of predators – predators have a keen eye for weaknesses in prey animals..
Rabbits can die of fear, but that’s sth that’s primarily seen when there’s a dog or other predators involved. Being chased by a dog or just having a yelping, barking dog hanging around the cage can absolutely stress a rabbit to death.
I don’t know what the cage noise/leg reflex was about. It doesn’t ring any bells with me. It doesn’t seem quite normal, but that’s difficult to know unless you were there and saw it.
I hope your male rabbit will be fine, it’s hard for a bunny to lose a bonded mate. He may become more interested in you, now when he’s an only bun. Try to spend extra time with him. Keep a close eye on his appetite and poop.