That might cause plot inconcistencies if not handled correctly. I'd say the easier way to handle it is just throw more clones at the group and leave the commander himself unchanged and more in the background role for this specific battle (yes, I know the focus should still be on him, but I don't see a better way around it right now for this battle, and it will still be from his point of view watching the battle unfold). Even if it's still not fair for my team, it could still lead to an interesting battle and show how cool that team of vampires/werewolves are as they stand on top of a large body pile letting lose a primal roar to the heavens.

Or maybe he did something to weaken your team? Like an...anti full moon or something super rare?