Nystatin is a very commonly used drug for birds with yeast infections, yes. So the treatment is standard. It works BEST mind you on an empty crop. But it will work with some crop contents.
Diflucan is really the better choice (as it doesn't require an empty crop). If she doesn't improve, ask him for it. It's the choice of avian specialists.
When you say he didn't empty the crop, and you referred to him removing contents of the crop, did he remove most or just enough for a sample?
As for her crop having contents, of course that will happen if she's eating. I would back up the treatment of the yeast infection by using probiotics. I would not use any other products (like apple cider vinegar) without consulting the vet. But probiotics work in tandem with the nystatin and he SHOULD have prescribed them, but then again most vets don't. Even avian vets, even avian specialists. If you ask about them they'll usually say "Wonderful idea!" and make you wonder why you pay *them*.
I want to send you a very good article on fungi (yeasts) in the crop. The thing about them - they're usually present in a static (slow/stopped) crop. The question is rather chicken/egg-like: which came first - the yeast infection, or the crop stasis?
Another thing about avian digestive systems... if the bird is stressed or ill or medicated, the digestive tract will slow down. The bacterial load in the tract will diminish to some degree (sometimes minor and insignificant, other times major and detrimental).
Better yet, it's important to know how the digestive tract of a chicken works. Simply put:
MOUTH (no chewing) ->
CROP (storage) ->
PROVENTRICULUS (some enzymes to break down via bacteria, light acid - very light) ->
GIZZARD (muscular walls and grit break down cell walls of plants) ->
INTESTINES (bacteria do the rest of the breaking down of food into absorbable particles, produce vitamins and enzymes, protect the system....absorbtion of nutrients happens here ->
CLOACA (remaining non-digestable material mixes with products of the kidneys and are excreted).
So you see, the majority of nourishment occurs in the intestines. If the bacteria are diminished by (insert whatever reason here) then the whole system slows down. When that happens, the crop doesn't empty. When the crop doesn't empty, food goes rotten and bacteria and yeast form.
Voila. Yeast infection.
Nystatin will treat the contents of the crop, although again it's best used on an empty crop. You can use it simultaneously with yogurt or another probiotic. Honestly for a true yeast infection, I'd hit hard and use a combination of not only Lactobacilli but also Bifidobacteria. That's the "magic bullet" for women's yeast infections which is the same (Candida albicans) as crop yeast infections. C. albicans is present in a healthy system - just not in the extreme blooms that cause the problem you're seeing.
If you can't get a probiotic capsule at the health food store for women's yeast infections (no joke here), try using simply acidophilus capsules or tablets from the grocer. You can also use plain yogurt, no bits please. Or you can use an avian-specific probiotic (but unlikely you have one sitting around) or a prepared probiotic like Probios brand dispersible powder. The latter is my favorite, but I've used all of the above with success as a general probiotic.
Also at this time NO solid foods unless they're easily dissolvable. Test: put the food in a glass of water. In ten minutes if it's not basically mush at the bottom of the glass, it's not dissolvable. You want nutrition to trickle down through the digestive system without having to rely on the gizzard right now.
Good foods:
her pellets - 90% of her diet at the very least.
a little egg yolk, boiled (not scrambled - the glass test fails) and mashed. Freeze what you don't use. Protein is acceptable.
Yogurt - 1 teaspoon per adult bird daily or so.
Babyfood applesauce: highly recommended in small amounts (1/2 teaspoon or so) as a cleanser of the digestive tract. (More on this below) Also acidifies the gut without interacting with the nystatin.
I personally would hold off on apple cider vinegar until after the course of Nystatin is finished. Then I'd use it (organic only because of the bacteria) at 1 teaspoon per gallon of water every other day or so until she's fully back on track.
Now the applesauce - I had a parrot who was diagnosed with a neurological disorder that basically shut down their entire digestive system to a slow trickle. The bird, while being fed even formula, had problems emptying her crop. A very experienced aviculturist told me the applesauce babyfood trick used on exotics sometimes. It cleanses the digestive tract, is already broken down mostly, is full of pectin which does the cleaning as well as feeding the GOOD bacteria. The pH helps make the tract healthy for GOOD bacteria = bad for yeast!
And good bacteria fight off yeast. They're your best friends in the chicken biz.
This is a lot of info so here's the summary:
Continue the nystatin, putting it the crop when empty if possible.
Feed only easily digested foods - that means no free range grass.
Feed probiotics daily during this treatment and for a week thereafter.
Don't put anything in the water unless the vet indicates it - especially and including vitamins. If you need them, feed them.
Follow up with your vet and absolutely do NOT expect him to be your bird's advocate. You are. For that reason, I'd like to share an article with you I think you'll find handy.
http://www.avianweb.com/candida.html
IN the mean time, sorry for the long LONG post here and my type-errors.
I hope you find the information useful.