I had a similar experience with a previous employer during my 2nd pregnancy. I worked in a dental office associated with a hospital. It did not start out bad at first, until I started prenatal appointments. I was scolded upon my return from those appointments. They wanted me to see a different dr who would see me only on weekends and not during business hours, which wasn't possible for me. Then they wanted a dr's note to prove I needed prenatal visits. I was formally written up and disciplined for turning in that dr's note.
Then my obgyn found out I was working in 92 degree heat because they did not have working ac and that I was not allowed my 2x15 min breaks at work in addition to the 30min lunch. I was beginning to show signs of swelling IE pre-eclampsia. I've never seen a dr get as upset on my behalf as that obgyn. My husband followed me to that appointment to make this clear to the dr. That dr's note (saying I needed to be off my feet during my breaks and the temp needed to be controlled) resulted in my work hours getting cut back to 2hrs a day for 2 months. I was fired when I returned after 7 weeks of maternity leave. The eeoc is/was a joke, there are laws but you can't depend on them. I couldn't afford a lawyer because of the lack of income at that time.
I hate to sound pessimistic but I just wanted to offer my experience. I did everything humanly possible to keep that job (practically begged and cried), it was steady work, with the best pay and benefits I've ever had. But the whole experience wounded me in a way that has taken years to come to terms with. I always try so hard to do right by others and to have gone through that experience was completely demoralizing. I would have been better off turning in my notice and seeking work elsewhere. Hearing what you are going through sounds so familiar to the start of what I endured that I worry for you.
I've come across a few webpages where people volunteer their time to help others with the process of fmla and lupus, helping your employer understand. Perhaps have a sit down with your supervisor and HR and try to be as straightforward and informative as you can be. Ask them what you can do to make this easier for them and let them know what is feasibly possible. If this fails, then perhaps it is time to look elsewhere.
Diagnosed with SLE lupus October 2014.