Thank you for waiting. It is very difficult to raise newborn baby rabbits with handfeeding, so I was hoping we might be able to return Baby to the mother, but when the mom kills and eats babies, obviously that's not possible. If this was the doe's first litter, you could try a second time because some young does will do this the first time and will raise their babies well after that. If she has killed other litters, then I wouldn't breed her again.
I'll give you a link in a moment that has very detailed instructions on caring for orphan babies. For now, I'll summarize. The acidophilus is fine. Goats' milk is the closest substitute for rabbit milk. You can often find it in health food stores. It is usually combined with some other ingredients, such as KMR to make a formula. If you've been feeding from one of the tiny bottles they sell for orphans, you might get better results by using a syringe. That's good news that the baby is going to the bathroom on her own. This site has detailed instructions on all aspects of raising orphans, including a recipe for the formula:
Since this little one doesn't seem to be growing, you might want to add a little cream to the formula. Too much is dangerous. Add about one tablespoon per can of KMR.
Overfeeding is one of the most common causes of losing orphan rabbits. Mother rabbits only feed their babies once or twice per day. With very young orphans, it may be necessary to feed more often, but after the first few days, it's best to go to a more natural schedule. At one week of age, the babies should consume 5-7 cc/ml at each feeding (two feedings per day). You don't want the stomach to distend too much. When feeding more than twice per day, divide the amount up between the feedings.
At two weeks, you'll go with 7-13 cc/ml each feeding. When their eyes open, start giving them timothy hay, pellets, and water, but do continue the twice a day feedings.
From three to six weeks, they'll need 13-15 cc/ml at each feeding. After six weeks, if they're eating solid foods well, you can wean them.
Sometimes there are babies that just fail to thrive, whether the mother is feeding them or we are. It seems they are born with a genetic defect that causes this. If the other baby you are raising is doing well, that may be the case with this smaller one. But I wouldn't give up. I would read the information on the site I gave you above, add the small amount of cream to the formula, use a syringe to feed so you can measure the amount, and make sure she is eating the proper amount at each feeding. You will be doing all you can, and then you'll just have to see what happens.
If you have more questions, just let me know. I hope both babies will thrive.