This is pure speculation but I am speculating that Peter uses the Machine and instead of destruction or creation merges both Universes and creates a new Universe in the process.
Where there where 2 now is 1 ; where there was 1 is now zero. The history of the new universe is changed to accomodate the merging.
Where there where 2 now is 1 ; where there was 1 is now zero. The history of the new universe is changed to accomodate the merging.
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