If Aeon has only been cloned once, how is she experiencing the same sanity-wrecking deja vu as the other citizens, which was all but stated to be caused by being cloned again and again?
The silent shorts are canon and she's actually been cloned multiple times?
Alternatively to her having been cloned multiple times, keep in mind that the primary "deja vu" which we are shown occurs because of triggers. To be sure, she is driven to find Trevor, but it doesn't seem to be either 'sanity-wrecking' or 'deja vu'.
Perhaps the Keeper has cloned her before to work as his assistant, keeping her hidden on the Relical, while the pair of them waited for Trevor to make a breakthrough that would allow the constant "recycling" to end.