Have you had another test done to confirm the negative? I think coccidia can replase, but I could be wrong.

It’s quite possible that because she had coccidia that her intestinal tract hasn’t quite recovered, or that it has damaged it a little which has resulted in her not being able to absorb as many nutrients from her food as she otherwise could. This in itself could lead to lack of growth and weight gain. I think coccidia is one of those things that while successfully treated, it can leave permanent damage.

Was bloodwork done? Did the vet say if it tge coccidia was affecting the liver or digestive system? Normally the intestinal coccidia, when present in very high numbers, results in runny/mushy stinky poop that can turn to deadly diarrhea quickly if not treated. Small dry poops are usually a sign of gut slowdown. It is true that damage can be done, during a spay/neuter, which can cause gut issues, “acquired megacolon” for example, which can also affect the ability of the gut to effectively absorb nutrients resulting in weight loss. Because there are a number of things with similar symptoms, it sounds like the vet may need to do further testing. I can’t help but wonder what bloodwork would show, and if there may be a different parasite at work in your bunny that maybe a different med would take care of, or a bacterial issue that a culture and sensitivity test may identify. Also, have you talked with your vet about probiotics?

Her intestinal microbiota could perhaps be damaged by the coccidia. Bunnies rely to a great extent on the microorganisms in their gut in order to absorb nutrients. The microorganisms in the cecum render the food digestible – as you know, the food must pass through the bunny gut twice in order for the bun to be able to take advantage all the essential nutrients.
Probiotics with live brewer’s yeast (saccharomyces cerevisiae) have been shown to help young bunnies gain weight. There are also probiotics that contain enterococcus faecium, the most prevalent bacteria in healthy bunnies’ guts.

I went through the same thing with a bunny I had a few years ago. She had to be put on benebac and also two other medications otherwise her poops would get very soft and mushy. The vet told me she just had too much bad bacteria in her gut flora. She also never grew and her weight did fluctuate. All our tests came back negative too and they never figured out what was wrong with her. I do believe this was the effects of her coccidia. The benebac really did help her a lot maybe you should ask your vet about it. Also we were instructed to give her critical care multiple times a day for the majority of the time we had her. When we started weening her off of all the medications and what not was when she had her final and most dramatic decline of health. But yeah, if you’re worried about her weight the best thing for that is critical care and benebac is good for gut bacteria which usually is good for balancing out poops.