I’m sorry to hear this. I have no experience with ear amputations, but it is fairly common that rabbits lose one ear or both or parts of them due to bites from another rabbit. Ideally the ear should shrivel up and fall off of its own (dry gangrene). If it’s wet you absolutely want to get it amputated, but your vet will of course know this. It’s not nice at all, but compared to the seizures and rolling caused by e cuniculi it’s really rather minor, but being one-eared is a cosmetic flaw of course. I’m guessing they needed to get the diazepam into him really quickly to ease the seizing and didn’t want to wait for the slower acting sub Q delivery to take effect?
4 weeks of fenbendazole is standard protocol for e cuniculi, but many rabbits also benefit from co-treatment with Baytril (according to Molly Varga, well-renowned British rabbit vet) even if the e cuniculi is caused by a single-celled microsporidian organism and not by bacteria. E cuniculi is still rather a mysterious disease that rabbit medicine knows a lot more about now than before, but still needs to know more about.