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I am sorry that you have been waiting for a response. I recently just logged onto the site and noted that your question hasn't yet been answered. I am a licensed veterinarian with over 25 years’ experience and would be happy work with you if you are still needing assistance.
It sounds like you are doing everything right. Unfortunately, the only known stimulus to muscle building is use of the muscles. It is interesting how quickly muscle atrophy occurs, but muscle regeneration can take a long time and even with hydrotherapy, she may not yet have achieved full range of motion in order to incorporate all of the muscles that were previously not being used.
Are you working with a veterinary physical therapist?
The best thing she can do is to keep those legs active and it sounds like you are doing a good job with that.
I hope this is helpful. Please let me know if you have ANY other questions. My goal is to give you 100% satisfaction and if you are not yet satisfied, please reply so I can clarify for you.