Why is your comm dying at a very pregnant moment?
Dismissing the dialog is minor compared to the Loop mode being overridden, being stuck in either Auto or Manual mode. That's what the Auto Tune dialog is trying to resolve, and why it cannot be dismissed, but is unable to resolve, hence the "can't exit" issue.
It's sort of like doing a Force, then losing comm. That is almost always not good, because you can't UNforce until you re-establish communications.