I've never had one spayed or neutered ... that is reserved for a life and death situation for me ... that is a very delicate surgery for small animals ... especially chinchillas, because they stress easily ...
BUT, as with any surgery, she will probably be put on antibiotics afterwards.
Antibiotics kill all bacteria ... the good as well as the bad. The good bacteria is referred to as "flora", and is what your chin needs to digest her food and keep her digestive system going ... including pooping which is a must for chinchillas.
With any of mine that have to be on antibiotics, I try to help replace the good bacteria several times a day. I do this by using yogurt (mine seem to like the strawberry and blueberry the best) and/or acidophiles. (Found in health food stores and must be refrigerated after opening.)
CAUTION: When giving yogurt, you must remember that yogurt is a milk product and must be given 3 hours before or 3 hours after the dose of antibiotics ... if not, they will cancel each other out and it will be as if you are doing nothing.
How many chinchillas has your vet spayed in the past?
Jo Ann