I’m very sorry you have a chronic illness.
My guess is your bun is being – a bun. Some rabbits are extra loving when their bonded mate is ill, some rabbits are completely indifferent, but many rabbits actually act out in the presence of a sick fellow bun. It’s quite common between rabbits -healthy rabbits can be really mean to poorly rabbits even though they’re very close friends (bonded).
This is of course about instincts, not concious choice. The rationale would be that it’s simply not favorable in terms of survival to be near a sick member of the herd. Sick individuals attract predators, because predators have a very good eye for weekness in prey animals.
Now, you are not a rabbit (obviously), but your bun might regard you as her bonded mate. If this is the case, your flare-ups could be stressful for her, since she regards you as a fellow bun. (Which is rather a great compliment to you, most hooms never get accepted as honorary buns).
She might get used to them with time, since nothing bad actually happens when you’re sick, no predators will appear and try to eat you both. Or the instinct simply runs so deep that it will persist.
I’m sorry that she’s being difficult during your bad spells.