User blog comment:FairyRaven/Fairy Tail Chapter 329: Seven Dragons, Review and Commentary/@comment-4933386-20130430130826/@comment-7418318-20130430135111

Actually the anime made Cobra's return more likely, since he willingly gave himself up to the council that time.

Also he didn't have that scar on his face in the Oracion Seis arc (neither in the anime nor the manga), but he did have it in the "Key of Starry Heaven" arc. That, along with the mention of the "Zentopia incident" by Yukino in the manga leads me to believe that even the manga consideres that arc canon, even though it was only shown in the anime.