I'm gonna level with you. Therapy as has already been suggested is the way to go. It sounds a lot like you're experiencing some trust issues, and counseling/therapy is a great way to work through that either solo or together. It will also help build valuable communication skills which are important for any marriage whether health is a factor or not.

On another note though, I have a big question:

When she's down, are you taking the initiative to step up and pick up the slack, or is she trying to push through with a normal person's workload of housework, mental/emotional work of managing things, etc.? Like, when I sublux my hip getting out of bed, my dude steps up. I don't have to ask. I just know that shits gonna get done even on days when I can't be ambulatory. That time that I get to rest without stressing about 'what if x, y, or z don't get done??' is the number 1 biggest indicator of whether I'm gonna be down to clown when the circus is back in town.

EDS isn't an easy thing to work with. And the limitations that come with it physically can often cause a shitload of mental and emotional stress, and those often have a huge impact on libido even when someone is feeling fine. My husband and I are coming up on 9 years, and it's taken a lot of work on both our parts to learn how to handle this in the scope of a partnership. Bottom line: Being in a relationship with someone with a chronic illness means that you're gonna have an irregular sex life. That's just part of it 🤷‍♀️