Hi there - I'm Dr. Sara. I'm a licensed veterinarian who works exclusively with dogs at cats and work but I have bred chinchillas and owned them as pets for years. I'm sorry that there was a delay in your answer here - I suspect the other experts might not have felt that they are well versed in chinchilla care. I've been on vacation the past week. I know that you may not need any information now, this late, but I also didn't want to leave you hanging!
Unfortunately, with a critter as young and frail as a chinchilla kit, there's not a whole lot that you can do other than give her time and TLC. Force feeding can help - oxbow critical care if she'd been eating solids a bit, vs milk replacer. Here is a website with general guidelines on nursing care for babies as well as a recipe for milk replacer:
If she's truly that much smaller than her sister, it's likely that she's not thriving, potentially due to a congenital issue (something she was born with). You're doing all that you can, short of finding a vet who is very experienced with chinchillas (they aren't common!!).
Keep her warm and give her access to move on and off of a warmed area of her box by placing a heating pad underneath the bottom of her enclosure.
I'm sorry that we can't be of more immediate and thorough help. Please let me know if I can answer any other questions :)