I'd say wait until tomorrow morning and see if there is improvement since chinchillas typically consume most of their food at night.
If there is not I recommend feeding half the manufacturer's recommended daily amount throughout tomorrow to keep her bowels in check. Then you can wait another day to see if there is improvement after that, however, it is likely the antibiotics are the direct cause of the problem and that it is going to get worse before it gets better.
I'm glad you are seeing improvement. It is possible the infection is being killed off by the meds and that could be the cause of her getting her appetite back. If so you'll find she'll probably eat a good part of her pellets tonight. I think the pelleted diet is still a pretty big percentage of a chinchilla's diet. I'm guessing it's around 50% of their typical daily intake by mass.