Be very careful. A site "..that is no longer up.." may just be undergoing maintainence, or is only down temporarily due to server problems. Does this program check for all these things? Does it know if the site is not there because there is a server error? For all you know, that site could return an hour after you deleted it from your Favourites and you have lost a good bookmark.
I would not get rid of good Bookmarks so quickly.