Ion and Sync are replicas of the real Fon Master Ion. When Ion died, Sync was a reject and Ion was chosen to become the Fon Master.
It's explained that Arietta loved Ion, but she didn't know that the Ion she loved had died, since Sync always wore a mask before falling into the Core. I doubt she saw Sync's face being similar to Ion's before, but Sync never wore his mask after Sync and Van came back from the Core.
Since Arietta was one of the God-Generals and were in on Van's plan, is it explained in the anime/manga how Arietta never knew that the Ion she loved had died?