I’m sorry you are going through this.
Rabbits can carry the EC parasite, (a very tiny parasite, nowadays classified as a type of fungus), for a very long time without showing any symptoms and without any complications from 5he parasite. Symptoms can also be atypical and mistaken for something other than ec, so many cases probably go undiagnosed.
The ec parasite lives inside the cells of the rabbit. The rabbit’s immune defense keeps the parasite from proliferating through mechanisms not yet quite understood. When something challenges the immune system, for example when the rabbit gets old or sth stressful happens (a really big molt can be enough), the parasite “seizes the opportunity” and starts making spores inside the cells where it resides. When the cell is full of spores, the cell ruptures and it is believed that it is the ruptured cells that gives rise to the massive inflammation that causes the ec symptoms.
It is currently believed that the ec parasite can’t be completely eradicated from the rabbit. Treatment is long, 28 days for starters, and recovery often take even longer. It’s recommended to do repeat treatment with panacur (fenbendazole) in the event of flare-ups and/or for 9 days every 6 months if a bun has been diagnosed with ec. (Some buns only ever have one symptomatic episode of ec, others have flare ups.) It is also important to bring down the inflammation. Metacam (meloxicam) can be used for this. For really severe cases, one injection of corticosteroids can be very helpful, but corticosteroids must be used with great caution in rabbits.
As for chlorox wipes, it’s safest to carefully clean all residue away from the surfaces you’ve used them on before letting the bun have access again. There are better products for disinfection, for example Virkon, which is non toxic to rabbits and odorless, and it doesn’t stain.