Have patience, anonymous, but keep allowing her to fly with her mother. It can take some time for pokémon to heal from trauma, but so long as your noivern is spending time with the pokémon who likely taught her how to fly in the first place, it’s probable that her healing period will go quicker than you think. Her mother will likely be able to sense her fear and work to correct this by herself; as both a maternal figure and a member of a species that relies on flight, your noivern’s mother will likely know best how to teach her daughter to embrace flying again. It’s important for you to give them space to do this but show your support for your noivern throughout this healing process.
If necessary (such as cases in which your noivern can’t move past her trauma), you may also want to consider allowing her to fly on short jaunts during the early evening as well, when it’s unlikely that she’ll be attacked by crobat (or anything else, for that matter). By “short jaunts,” I mean “anywhere you can watch her.” If she has the comfort of someone who cares for her, she’ll be able to grow back her confidence to fly on her own.
Either way, it will be a gradual process, so it wouldn’t be at all unusual if it takes your noivern months to gather up the courage to fly on her own again.