User blog comment:IamJakuhoRaikoben/Chapter 503: The Last Sight Seen, Review./@comment-7418318-20160928235211/@comment-7418318-20160929144840

Mira has been defeated several times and never lost any of her captured souls.

And then there's also Dimaria's comment about Natsu's power surpassing that of a God, which sounds like she still has the power of a god inside her, but Natsu still whacked her.

Combine those two and I'm quite sure she still has the Take-Over, it just wasn't enough to get Natsu.