Well at some point un the Archie Comics. Eggman grew more and more obssesed with sonic. He tried his best in one last battle to defeat him…and lost. That defeant was the final straw and the bad doctor went bananas.

He didnt amnesia per se. But his insanity made his memory to go back and forth to different stages in his life.
And some point he recovered, and came up with the idea that he always failed because the cintinous exposure of sonic to Chaos Energy made him a "probability changer" that would always find the tinniest chance of his plans to fail and make it so. So he decides de "restart" the Universe to make Sonic "Chaos Factor" go away.

Sorry for the long post but I loved that era of Sonic comics.

Is it me or eggman in the last panel kinda looks like this