You wrote that you downloaded your tree from Ancestry.com, but the result sounds like you created a new tree at Ancestry.com by uploading an FTM 2012 file. That's the only way that the comments and "origin" information for media files would have been deleted. These things don't synchronize with Ancestry.com. If you want to preserve them, you must treat your tree at Ancestry.com as your primary tree. In the case of sync failure, you must re-download that tree from Ancestry.com. (N.B.: when you do this, you lose everything in FTM that doesn't sync with Ancestry.com. That can potentially be a lot of work, so beware.)
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