Some people think Amy has been taken since halfway through season 5, since “River is the only water in the forest - the forest on the spaceship -
AmyPond was in fact, already a flesh copy as seen in The Rebel Flesh/The Almost People.
Look at this:
And then.. look at this comment:
I just realized that the title of the second episode of the Byzantium storyline (S05E05) was “Flesh and Stone”
Flesh and Stone
FLESH AND STONE
EVERY VICTIM IS RORY. EVERY SINGLE TIME.