I don't make it onto the forums very often, so am weighing in kind of late on this thread, but maybe some of my thoughts will be helpful. I'm very puzzled as to why the vet prescribed Baytril, if all your chin had was gas issues, and a bit of soft poo. My chins were never able to handle Baytril, as it's so hard on their gut.(Trimethaprim sulfa was the only antibiotic I ever had any success with). If there are no bacterial issues, why prescribe an antibiotic that will only cause further stomach problems(such as lack of appetite and gut flora imbalances)? The vet's dietary suggestions lead me to believe he/she is confusing chinchillas with rabbits or something...quite bizarre. I would suggest you cast your eye around for another exotic vet, if it's feasible. Do buy a copy of The Joy of Chinchillas, available on the California Chins website. It's a huge help and will give you a lot of info on raising chins. There are other helpful books out there, but this one is a must.
I noticed that a lot of my pregnant chins would increase their water intake the month before and for awhile after birth, and their poos were often big and soft. Usually, this goes away by itself, but if it becomes too messy, I would give acidophilus and make sure there was lots of fresh hay to tempt her. Pregnant moms and new moms love yogurt, which I would feed them via syringe, just to make sure they were getting enough calcium.