Im sorry to hear about your bun being sick. I just went through this with my bunny and he is still recovering from the head tilt. The thread that Luna posted was started by me when Blu started to show signs of something being wrong.
Don’t be afraid to question your vet. I did with mine and also brought up ideas of meds to give him from reading people’s post. As far as the not eating much, I am not sure because Blu never really lost his appetite except one time when I doubled dosed his medicine on accident.
I can tell you that Baytril did not work for Blu and it was SMZ TMP, and Panacur that showed signs of improvement. My problem was just being patient because I wanted results right away but it does take time. Blu is back to normal now, other than his head tilt but he has adapted to it very well (its slowwwwlly getting better).
Is your vet rabbit savvy or do they just see them every once in a while. Is it the same vet from when you took him to the ER? Because I have noticed when I called around for a 24 hour – ER clinic (when Blu gave me a scare after my vet closed) that those vets see rabbits but do not specialize in them. Also, you said that he is on something similar to critical care – if that isn’t working you could try the actual critical care brand. They make a banana flavored one that Blu could not get enough of.