Google Reader doesn't provide a way to delete an item (article), so when you delete an item in FeedDemon, FeedDemon simply ensures that the item is marked read and unstarred in Google Reader to prevent it from reappearing as unread or starred. However, this may mean that it does reappear as a previously read item.
Keep in mind, though, that it's not necessary to delete items since older items are automatically removed from both FeedDemon and Google Reader. Rather than deleting items, we recommend simply marking them as read so that they no longer appear in FeedDemon's default "Unread or Starred" view, and then letting them eventually disappear completely.