My daughter has been injured more times than I care to count starting when she was a Level 9. But through all her injuries (except surgery where she stayed at home for two weeks until cleared by her doctor to do some conditioning), my daughter went to gym and trained/conditioned all on her own. Her coach never helped her with conditioning or training whilst injured, so it was up to her to stay in shape.
If you are in a good gym with experienced coaches, they usually have a training plan for injured gymnasts. Perhaps because my daughter has had so many injuries in the higher levels (9 and 10), she has figured out what she can or cannot do. She usually did a lot of rope climbing and core exercises. She worked on her splits (she sat on oversplits for longer periods of time) or improving her flexibility. She used thera bands for stretching and strengthening exercises. She did a lot of handstands (if your daughter can't hold it for long periods, she can do this against the wall). There are also a lot of upper body exercises, push ups, pull ups etc. While she did not have enough exercises to fill the four hour practice, she did as much as she could. She also did cardio on a bicycle at the gym when her injuries allowed. On the later stages of her recovery, she joined the team in whatever she could.
I never told her to keep up her conditioning, she did it all herself because she wanted to. Many girls don't care to keep up their conditioning, but I think when you hit Level 9 and 10, it is vital to do so.