Before we will see the way to delete secondary tiles, I strongly suggest you to read these two articles

Live Tiles in Windows Phone 7.5 or Mango phone

Restore and Preserve Page State for Windows Phone 7.5 or Mango Phone

Assume we are navigating to a page called Page1.xaml from the secondary tile.

A common requirement you may come across to delete the secondary tiles once user has navigated to the application page.

Essentially you need to perform two steps

1. Query for the secondary tile and delete it
2. Perform delete operation on OnNavigatedTo function of application page

Function to delete the tile

private void DeleteTile()
        {
            var uri = new Uri("/Page1.xaml?state= Live Tile", UriKind.Relative);
            ShellTile tileToUpdate = ShellTile.ActiveTiles.Where(t => t.NavigationUri == uri).FirstOrDefault();
            tileToUpdate.Delete();

        }

Simply we are querying for the tile and then deleting it.

Calling it to OnNavigatedTo function

 protected override void OnNavigatedTo(System.Windows.Navigation.NavigationEventArgs e)
        {
            DeleteTile();
        }

This was all required to delete secondary tiles.

I hope this post was useful. Thanks for reading