Indexing problem, please help !!!

almost one month i had edited my permalinks from ”category/postname”,
to ”postname” this resulted in more than 180 crawl error in my webmasters account, my website traffic went down to almost zero.

and again i changed the permalinks to category/postname thinking it will improve my crawl errors but, its of no use instead i m getting same errors.

and above all my website was penalized for the duplicate content. all coz of this permalink trouble,,, would any 1 please help me out of it..