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As I understand it, Giovanni is not from an alternate universe, meaning he never actually beat Red, this is just his big comeback.
This means that Red, Ethan and Lyra never lost.
Although keep in mind, every single protagonist exists in each others universe, so for example; In the Archie-won universe, every protagonist technically has to suffer the consequences of the expanded seas. This just means that, in relation to the "Legion of Doom", Red, Ethan and Lyra did not fail and contribute to the villain alliance.
The rest of the protagonists however, well...
