User blog comment:D. Cello/Assassin's Creed: Revelations (PC) - Official Assassin's Creed Wiki Review/@comment-187.105.170.237-20111221184831/@comment-5503561-20111222175558

You know, it's pretty obvious Altaïr couldn't have sent his apple to Cyprus, even before it was shown in Revelations.

Altaïr gets the Apple from Al Mualim and keeps it with him pretty much for the rest of his life. It's not sent to Cyprus, and the Codex is an effective decoy to keep people from Masyaf. Eventually it ends up in England. Fast forward, Abstergo finds it and loses it in Satelite incident. Lucy explicitly states that apple was the one from Masyaf. Therefore, it couldn't have been sent to Cyprus, only to be locked away beneath the Colosseum by Ezio and found intact by Desmond. It would already be lost in the accident by then.

Sima's theory about Templars coincidentially finding another apple on Cyprus itself by following the codex is most plausible.