Board Thread:Questions and Answers/@comment-26126387-20150526202422/@comment-27403314-20150629165212

Yes, they are enemies, but at the same time friends. So they're frenemies.

About the episode, note that Cowbot was programmed to destroy Sonic, so when reversed it would go destroy Eggman (aka kill him), and surely the Sonic Team wouldn't want Eggman to be killed by his own creation, since it isn't right to do so anyway.

Sorry if I didn't explain it clearly. :/