Will I Be Able to Play the Flute with Invisalign?

But you'll need to retrain your lips to direct the flow of air into the mouthpiece. Its totally doable and shouldn't be a problem. I know saxaphonist that use invisalign but they are reed instruments.

One SHOULD be able to learn to blow with Invisalign in place, but it will be awkward at first.  If the usage will only be for about an hour at a time, it should be ok to remove Invisalign for that period of time.  If you are playing for several hours per day, it may be worth it to learn to use them.