Why did the vet say that an antifungal med would help to stimulate her appetite? It will do the exact opposite, antifungal meds are very harsh on their gastrointestinal systems to begin with, and since she has a confirmed bacterial infection and has to take the antibiotics, adding antifungal meds on top is going to make the problem much worse...Unless the vet properly diagnosed and confirmed for sure through testing (cultures) that she has a fungal infection in addition to the bacterial infection, I would definitely hold off on giving her the antifungal med, as it will do nothing to stimulate her appetite and will make her feel much worse. She has to have the antibiotics, because I believe she was diagnosed through testing to have a bacterial infection, correct me if I'm wrong about this...
The soy yogurt with active cultures/probiotics will be what stimulates her appetite, as I mentioned in my first post probiotics are amazing for sick animals and people with upset gastrointestinal systems, and can also help beardies who are impacted because they replace all the normal, healthy bacteria that should be living in her gastrointestinal tract.
As long as the yogurt you are giving her is a non-dairy, soy based yogurt that says it has added active cultures or probiotics on the label, then yes, I'd feed her as much as she'll eat in one feeding, and I'd do it twice a day until she starts to eat on her own and her poops are normal in appearance and frequency. Non-dairy soy yogurt (as long as you choose one that says it has live and active cultures or probiotics) is good for her, it will not hurt her at all, and in addition to the probiotics settling her stomach and replacing the normal healthy bacteria in her gastrointestinal tract, most brands also contains added calcium, protein from the soy, fluids, etc. All of which she needs. I stopped eating all red meat and pork products along with no soda or Fast Food about 15 years ago, and I started using soy milk on my cereal (I eat a lot of cereal daily) at the same time...I usually use Silk brand soy milk because all of their products have added probiotics in the same amount as Activia yogurt, which is dairy yogurt made especially to be a source of probiotics. I also eat a ton of yogurt, I used to eat the Silk brand soy yogurt and it's loaded with good stuff for her. I now eat dairy yogurt, usually Greek yogurt, but I can attest to the probiotics in any type of yogurt helping to make my stomach feel much better if it becomes upset. I used to take a probiotic supplement tablet every day, but now just eating 2-3 little containers of Greek yogurt per day does the trick, and I also get my Calcium at the same time.
I don't know why the new trend with vets (especially reptile vets, I haven't seen this at all with any avian vets) is to prescribe sick beardies antibiotics, antifungals, antiparasitics, or any combination of the three, without having any diagnosis at all, sometimes it's even without running a single test, like a fecal, and it's usually explained to the owner that we'll put him on these medications "just in case" he does have some type of infection or parasite. It seems that exotics vets and general vets don't understand how hard these meds are on beardies, and how they usually make their appetites worse. My advice to everyone with a sick beardie who goes to a vet is #1 try your best to only take them to a certified reptile vet or a reptile vet with a lot of bearded dragon experience, and #2 refuse to put your beardie on any medications without doing proper testing and getting a definitive diagnosis. Reptiles recover from illnesses very slowly, so if a vet guesses what's wrong and gives them a broad-spectrum antibiotic to take for a month, and the antibiotic does nothing but make the beardie worse after a month, then they go back and this time they give them another round of a different broad-spectrum antibiotic plus they add an antiparasitic med as well, then those don't help after another month, and the vet then after 2 months when the beardie is now critically ill, has lost a bunch of weight and it
black bearding, then they decide to run a fecal, cultures, or blood work and find out the poor beardie has a yeast infection in it's gastrointestinal tract and has to take another month of the actual antifungal med that will help them.... It's just so unnecessary and a waste of time, money, and possibly results in the beardie dying. I'll stop my rant now, lol, but this is getting more and more commonplace, and it's so frustrating because if they had just run the $15 fecal test first thing they would have been well months prior...UHG. OFF MY SOAPBOX NOW...
Keep us posted on how she's doing, but I agree that you should give the antibiotics to treat the diagnosed bacterial infection, hold off on giving her the antifungal med as it will not stimulate her appetite at all but just the opposite, and try a week of daily probiotics through the non-dairy soy yogurt a couple of times a day, and see if her appetite picks up after a week on the probiotics.
Can you post a few pics of her as well as her set up ? 
