Ivermectin is used to combat a parasite that causes River Blindness in African countries. I am not saying that is what the problem is, I am just saying that if it is a parasite that has migrated to the eyes, Ivermectin may help. I would contact a Vet though. Proper and sufficient dosage would be very important to stop the progression of whatever it is.
That's an interesting point about both parasites lodging in the eye, especially since researchers are not completely sure what they're dealing with.
E. cuniculi was originally classified as a protozoan. I think current consensus is "microsporidian," which doesn't get you that much closer to a truly helpful definition since there is ongoing debate about how they fit in the Linnaean system of classification. Most of the recent stuff I've read is calling them a fungus, or a group related to fungi.
This seems to be a pretty good review of the relatively recent research on
E. cuniculi, though it was published in 2014, so there may be newer studies:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7337189/
I don't know if a vet is going to be of any help with figuring out a dosage for ivermectin since it would be an off-label use of that drug. Fenbendazole (one brand name is Safeguard in the U.S.) is, I believe, more commonly recommended, though again, I'm not sure if a vet will prescribe that or not. I don't take my rabbits to the vet since there really aren't rabbit-savvy vets around here, and I cannot afford them anyway. And both drugs are available OTC. My suggestion would be to look up normal rabbit-safe dosages. Here's a thread:
https://rabbittalk.com/threads/ear-mites-please-help.36834/post-357320
I can report that I have had success in relieving symptoms I suspected were due to
E. cuniculi with three different drugs: ivermectin, fenbendazole, and neomycin sulfate. Both ivermectin and fenbendazole are anthelmintics (wormers) but have also been shown to have therapeutic effects in a broad range of other problems.
Fenbendazole is known to have anthelmintic, antifungal, and anti-cancer actions:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3580766/
https://www.oncotarget.com/article/28014/
Ivermectin was originally investigated as an anthelmintic but has also been indicated as a useful antibacterial, antiviral, anticancer, asthma, epilepsy and neurological disease treatment:
https://www.nature.com/articles/ja201711
Neomycin sulfate is an old antibiotic used in both humans and animals for infections in the gastrointestinal tract.
My suspicion is that each of these drugs may have different roles to play in suppression of
E. cuniculi, a parasite of the kidney, eye, and/or CNS, with the drugs possibly acting directly on the parasite, or impacting other, related problems.
From what I've read, no drugs have been found that actually eliminate
E. cuniculi, rather they suppress its over-proliferation. Internationally, veterinary studies have estimated that 40%-80% of pet rabbits test positive serologically for the presence of/exposure to
E. cuniculi, with only a few rabbits suffering symptoms.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7337189/