Issue with SmartCrawl no index setting.

I have upgraded several sites to use SmartCrawl from Yoast. I have a sneaking feeling when doing the migration, it turned all pages to no index. Several of my key profile websites have all been removed from Google.
When I checked today, it showed the SmartCrawl - Title & Meta setting was set to NO index. I think it is the migration process. Maybe, Yoast is tricking SmartCrawl to do this? I don't want to point fingers or assume - but it *seems* like the case. Please check and help.