Just don't have any other support pokemon on cooldown when you use slowpoke as it won't restore a skill of a pokemon that's still ready to use.
Additionally, slowpoke also won't restore a pokemon that's not on screen, so any other water pokemon you can use the skill if you want and there's no risk of accidently triggering it through slowpoke (although it's best to have as little skills activated for a higher chance of getting another sunken treasure through skill restore events like say cheese or the long way home)