I defeated skylar before going to the tower and now I can't get sklar to appear outside her gym, where the professor also appears, any ideas ?
Head to the Celestial Tower to the north. You will find the Professor on the first floor.
I first went north to celestial tower (same area as white 1). I talked to Juniper and beat all the trainers and rang the bell. After that I beat Skyla. Once you're done with both head to the cargo center and Skyla will fly you to Lentimas Town along with Juniper and Bianca