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Mary, Thanks for reaching out to us!  That is a good question!  Our crawler can only crawl sites that are indexable and that are public, so if you set the report to run against the starting URL for the new folder, it would try to find that folder if it is public.  One thing you could try out is to set your site public right before a crawl date, then immediately close access to it, this is the only way I can think Roger would be able to do it I am sorry that I can't offer something better, I hope that helps! Best, Peter Moz Help Team.