Dogs are predator and buns are prey, it really is as simple as that. Slow introductions. It might not work out, and you might have to face that. I know buns can coexist with other animals, but primarily there’s that whole predator prey relationship that makes it difficult.

You need to have a space that she cannot fit so he can escape when he needs to. Youll only train him to become aggressive towards dogs. Not keeping her away from him, youre only heavily stressing him out. Enough stress can cause sickness and death in rabbits.

Maybe the chihuahua just wants to play, maybe the chihuahua is responding so something of a predator instinct.  Anyhow, Joe, the Flemish weighing in a 15 or 20 pounds can easily defend himself against a 5 pound dog.  As a boy we had a male New Zealand rabbit….probably something like 10 pounds.  We had a beagle, who weighed substantially more.  Anyhow the beagle started bothering the New Zealand one day, it started nuzzling and pawing at the rabbit.  I watched in apprehension fearing the beagle was going to bite the rabbit…then suddenly there was a loud bang……the New Zealand rabbit gave the dog a very strong slap in the face with a hind leg.  No more problem from the dog.   Rabbits have a kick that is much stronger than you’d suspect.  Your Flemish rabbit, with 15 pounds of weight or more, has a good bit of that weight in the muscles of it’s hind legs.  My Flemish girls, 15 pounds, have heads and shoulders slightly larger than a normal rabbit, with the bulk of their weight in their hind quarters.  Maybe your Flemish Joe is a lover and not a fighter.  He maybe doesn’t know how strong he is.  I think a problem is that if he ever kicks the chihuahua in the face, he may seriously harm the dog. 

Dog’s respond well to scolding.  Scolding the dog when he chases the rabbit should work. Your chihuahua needs to learn it’s not a good idea to pester a male 15 pound rabbit. .  

TRAIN.
THE.
DOG.