So, the Scratch changes the order of the meteor arrivals, got you. But does it reset the universe in the process? Like lets say I have the A aliens species and the B species. A plays the game but the decide to scratch, would that instance of the universe be deleted (and thus new copies of B are created) or just the A planet changes?

The original Universe still exists. The Genesis frog holds all instances of a Universe so both can exist at once. For the kids, the B1 Universe was in the Genesis Frog’s Right eye while the B2 somewhere else within the frog, presumably in its left eye.

Mediums however are erased in the event of a Scratch, that’s why the kids had to book it out of theirs asap.