If you’ve got a pokémon with the special ability Lightning Rod, ensure your vaporeon sticks to them as much as possible. That should keep him safe, regardless of what happens during training. Additionally, take this as a blessing in disguise of sorts: use your vaporeon’s newfound strengths to your advantage. (That is to say, partner your vaporeon up with your other electric-types on the battlefield, as electric’s biggest weakness, ground, is no match to your vaporeon’s water-based abilities.) Finally, if possible, obtain and grow wacan berries, as these can decrease the effectiveness of electric-type attacks. Your vaporeon may benefit from holding them during training sessions as extra protection.
Otherwise, the only advice I can offer is be extra vigilant about keeping an eye on your team and ensuring that their abilities are kept in check. I know that’s not particularly helpful advice, but it’s probably the most practical for this situation, I’m afraid—terribly sorry about this!
Best of luck, anonymous!