Ok, thanks for the replies. Has nobody had any experience in trying it? I have found this piece of information on deleting content, but don't know how will it be after the transfer tool gets used:
http://www.ehow.com/how_2384430_delete-redownload-virtual-console-game.html
My 1000th post: https://gamrconnect.vgchartz.com/post.php?id=9368779