You should remove your aligners when you brush, floss, drink anything but water, and eating anything (including lollipops). Even more important with sugar since your teeth will decay during the invisalign process
Can I Have a Lollipop with my Invisalign In?
Doctor Answers 3
NO Lollipops with Invisalign In
You should not eat nor drink nor suck any solid foods or any liquids with sugar while wearing Invisalign. Your teeth will ROT!
Doing this once in a while is fine. Try and remove the trays ASAP and rinse with water. Then brush as soon as possible. Do not do this all the time because sugar not good held against the teeth. Us common sense.