User blog comment:JAlbor/Wikia at E3 2012/@comment-4681429-20120523203047/@comment-1153722-20120523215739

Ubisoft hasn't given any official word on it yet, and I think it's mostly me here that tries to fit all the pieces together regarding the canon and make sure that we get it right on the Wiki... I tend to get small things wrong a lot though (like Hitler being a Templar puppet instead of an actual Templar).

But if you fit all Pieces together, then Altaïr's Apple was never sent to Cyprus, he made people believe he sent it to Cyprus or Cipango (Japan) or that he dropped it into the sea. (If you take a look at the Codex, in one of the latest entries Altaïr says that he will send it to Cyprus but in the very last entry he still has it with him.) Seeing as Altaïr's Apple is referred to as Piece of Eden no.2 in AC1 and Piece of Eden #2 is also shown in the Glyphs in AC2, Altaïr's Apple somehow wound up in to the hand of Queen Elizabeth I of England and later Mahatma Gandhi, before the Templars got their hands on it.

Ezio's Apple must be a different Apple that coincidentally was on Cyprus, or (seeing as it isn't shown on the PoE maps) perhaps transported to Cyprus between 1191 and 1486, though whether or not Altaïr had it as well isn't sure. Two things that are noteworthy: in Revelations, Altaïr says "This Apple must not be found," with some emphasis on "this." In the Revelations novel, when Ezio finds the Apple, he says "and now it's twin!" (It referring to the Apple of Eden.)