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I had success separating them when they were young. The males usually aren’t interested in the females until they get to a certain size.Separating them does not make much difference with guppies. Female guppies store sperm even bette than female chickens.
As a practical matter, assume that if a female guppy has EVER bred with a male, that she will keep having one batch of babies after another for her entire life. And if it doesn't really last through her whole life, it certainly does last long enough for some of her sons to grow up and start mating with her, so then she's having babies again anyway.