THe family Medical Leave Act should protect you here. It's federal, I believe. The only thing you have to worry about is if you are considered a "Key" employee. There are levels of disability, too. The one I am on is a severe, chronic medical condition that entails periodic days off. I can get them without pay, and the doctor's note covers me for this. Ask your doc to cover your worry about the 12 hour shifts in the note. I think the supervisor has to listen to HR, who has to go by the FMLA. THey can't fire you if you're covered for disability. YOu're allowed 400+ hours a year for it, and then there are LOA's that are possible. See about how they handle the FMLA. You've been out, so it's possible you've used up the 400 hours.
HR sounds like they are with you on this. They HAVE to follow the procedures they have in writing, and these policies almost always are. If they don't you can sue them.
"Our greatest glory is not in never falling, but in rising every time we fall." -Confucius