Annulment doesn't touch on the legal status of marriage, so it's not clear how the Pope's doing that would change MIchael's guardianship.
Also finding a marriage null is not based on the current behavior of the spouses but on what was going on when they got married. As simple, clear examples, if the couple were found to be brother and sister, unbeknownst to them, the marriage is flat impossible. Or if one was hypnotized and therefore was unable to make a free act of will, then there is no marriage.
So the argument might run along the lines of, say, "Michael's subsequent adultery shows that he never intended the unconditional commitment necessary for matrimony, therefore there is no marriage." Maybe something like that could fly. But even the Pope can't just erase a real marriage just because it goes bad.
Can anyone honestly say that an annulment would hurt? It would only help.
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