Ok, here's my train of thought. Please interject if there are any points you disagree with.
Shadow can stop time for her using Chaos Control
Regeneration cannot take place while time is stopped.
Destroying her brain or heart kills her for death battle purposes. This is normally impossible due to regenerating faster than damage can be dealt, needing a special macguffin to overcome the regeneration.
So if Shadow stops time and carves out her heart while she can't regenerate due to the time stop, that's a victory for Shadow.