Lynda, Have you downloaded the spreadsheet?
When you do that you can whack everything down on mass but in the new interface layout when you add a new redirect you can add a file name which doe not exist in there too.
Goolgle can slap you on the wrist if it realises those pages never existed and your trying to do redirects.
I have a similar issue.
We are negotiating with a client who has a ecommerce site on ZenCart, a php opensource cart. He has been running this website for a while and is concerned about drop in rankings if he moves to BC. Please guide how we can convince him, and also maintain his SEO after moving to BC.