Flagyl is used for flagellates

But it also has anti-bacterial affects

Ive heard by a number of sources that RI's can be the byproduct of a Flagellate infection. Whether they are the cause or if they weaken the immune system to allow naturally occurring bacterial to grab hold and cause an Ri, I'm not sure.

But if antibiotics haven't worked, I'd try that

Or consider Mycoplasma and grab for the Tylan

I'm not a vet so any ideas I have are just that. All actions should be discussed with your vet first.