The Wind Warriors were responsible for the creation of the universe.
Both the comic and the game imply that they're given the task of providing atmosphere on lifeless planets. It wouldn't be a stretch to assume that they played a role in shaping the universe as a whole. Zephyr and the Wind Warriors successfully manage to rebuild everything they've destroyed
This could explain why you're able to replay the game's levels with no signs of environmental destruction. Omegaton attempted to cause an extinction of two entire elemental races.
Why else would Omegaton want to banish the Stone Stompers and the Water Whirls, the two who were associated with Omegaton? He forced the Stone Stompers to sleep in an eternal slumber while the Water Whirls were entrapped in a water bubble on Earth. Omegaton's plans however, failed as the Stone Stompers and Water Whirls were alive. His banishment though, resulted in the two elemental species suffering from amnesia.