Although i am not sure what you aim to do, i guess you want midi to transcribe the music she play, or do you want synthsound out instead of the pickup sound?
There is today software that will convert "audio" pickups/mics to midi in realtime, never tested any though.
Maybe you could test something like this?
https://play.google.com/store/apps/details?id=com.finestandroid.voicetomidi&hl=en_US&gl=US
But i had guitar synth devices Roland GR that could be hooked up to midi synths via midi.
But i guess this some sort of flute, and i am not sure a guitar syntn "module" would pickup right frequensies?