You said your rabbit has e. cuniculi? That is a serious disease in rabbits. Did you have her checked by a vet?
If that is the case, the only true way of getting rid of her watery eye is to directly treat the e. cuniculi. I do not really remember much of my research but I seem to recall it is very hard to treat. You will more than likely have to work with a vet for this, because I don't think you can get any of the medicines they use for it over the counter. Plus, it is much more serious as this effects not just the eyes but the nervous system and even in some cases the brain. (Again, I'm going off of bad memory of old research and a quick google search a minute ago).
Her eye looks like it's 'balding' because it's so watery the fur is being pulled away from her eye. That, and/or due to any rubbing she might be losing some fur. Someone on here recommended to me to use warm chamomile tea bags to relieve irritated eyes, and that might work for your bun. It also helps to take a soft towel or some paper towels and do your best to dry/clean up the discharge from the eye so it doesn't create worse problems.
Again, if it's true your bunny as e. cuniculi, her eye is only a symptom. The only true way to get rid of it is to take her to the vet and see what can be done. I'm sorry to hear your bun isn't feeling well, and I wish you all the best!