Nick,
Q1 statement is False. BOP doesn't actually delete confirmations until it is completed. It then performs updates, which may or may not delete or change existing confirmations.
However, you can make BOP 'behave' as if it first deletes all confirmations, by selecting "New distribution" on the parameters process tab.
The same sequence of checks configured in the Check Instructions is normally followed in BOP as well as during interactive ATP checks.
Best Regards,
DB49