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As far as we know, Amy only found that out when Mels (Melody's 2nd incarnation) regenerated in "Let's Kill Hitler" into the incarnation she (& we) already knew as River Song. Vastra & the Doctor had learned about Melody's Time-Lord-like DNA in the previous episode, "A Good Man Goes to War", but neither Amy nor Rory were present when they did so. Melody's parents both showed bewilderment when she regenerated, indicating that they'd not been warned that she might be able to do so.