Possibility 1: This isn't the first time Archer has been summoned to the HGW and has had to deal with a Sakura who's gone insane. As a Counter Guardian who exists outside of time and is summoned endlessly to resolve disasters, he may of even encountered it more than once. Encountering this scenario sparked a memory of it.
Possibility 2: The unknown "Route" that Archer originally went through had a series of events that forced him into a situation where Sakura had to be put down.
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