Go back in time and cut the tree. Go back and than go to route 2. go into the building and collect the notes. Go back into the past and plant the tree. Go back to route 2 and go along the top path where you cut by Amethyst Cave. You will see a guy who is trying to study Flabebe but he does not have his notes. Give him back his notes and he will leave, thus allowing you to catch 3 Flabebe.