Sometimes Baytril can affect a rabbit’s appetite and their GI system, so it can be helpful to give a probiotic with it, such as Bene-Bac Plus. That helps to keep the flora in their GI system at a normal level. Are you feeding her the same brand of pellets that she was used to eating? Sometimes rabbits are reluctant to eat a different brand. She also needs to be eating as much hay as possible. Since she is young, she can have alfalfa hay, but it would be good if she also had some timothy hay, orchard grass or any of the grass hays. You might need to try some different types and brands to find one she really wants to eat. It’s good that she is pooping, but it may take a little while before her appetite returns. So you would have to continue with the Critical Care if she is not eating on her own.
Regarding introducing her to your male rabbit, at 11 weeks old, Nala will be soon entering sexual maturity. If she gets cured of her snuffles, you could try bonding them now, but you would have to soon separate them and have her spayed, then re-bond them after she has recuperated. At this point, it would probably be better to keep them apart and wait until after her surgery to bond them.
Here are a couple of good articles on bonding:
https://binkybunny.com/BUNNYINFO/tabid/53/CategoryID/9/PID/940/Default.aspx
http://rabbit.org/faq-bonding-multiple-rabbits/