What you want to do is add a state change with the elemental skill, and have that state effect what element they are now weak to. First, create the state that you want. For that water spell of yours, you'll want to make a state that simply lowers the lightning element defense for two turns with 25% chance. Then, make a skill that deals water damage and applies that lightning weak state. You can do all of this in the database. :3
Edit: Actually, I'm wrong. You can add defense but not weakness in the state tab. Give me some time and I can find a way for you.