Clear Duplicates also deleting watched status?

I had some duplicates that had appeared and when I googled around looking for a way to delete duplicates and I ran accross the option to "Clean Video Library" So I thought perfect and when I did that it did in fact delete all duplicates however all the tv I watched and marked as watched decided to become unwatched.... It is a bit of a hassle to the users of XBMC. It would be much appreciated if you could tell me how to delete duplicates without changing watch status. Thank you.