Can you evolve more than one Kubfu after clearing a tower?

Yes, but only at the Tower that you cleared.

After clearing the Tower with your original Kubfu, you can re-enter it and advance to the top of the tower without talking or battling to any NPCs. The other Kubfu you want to evolve must be at the front of your party and out of its Pokeball. Go to and select the scroll. The game will ask you if you want to evolve your Kubfu. This Kubfu can evolve regardless of its level or happiness value.

This only works at the Tower you cleared. You will not be able to enter the other Tower; a NPC at the other Tower will prevent you from entering and hence evolving Kubfu into the other form.

Note that you cannot obtain a second Kubfu in-game. Any Kubfu other than the one you obtain through the story must be obtained through trading.