User blog comment:Master Sima Yi/Assassinews 02-03-'12 — Leaked AC3 info!/@comment-3979092-20120303000936/@comment-1888015-20120303013754

Supposedly, the Apple that they had was the one left at Masyaf at the end of Revelations, which is why they needed the locations of the others to help them get another. With ACB revealing the one at the Colosseum and Lucy's death, Abstergo couldn't get Ezio's apple.