Well I don't have any save progress on my DSi titles I bought since when you transfer the games from DSi to 3DS it automatically deletes your saves (Thanks Nintendo!), so that won't really be an issue. Just out of curiosity if you called Nintendo and claimed that your old system was lost and they unlinked NNID with your old system, couldn't you have games on both the old system and new system?
Doubtful. It might work for a while, idk, but if you ever wanted to set up a NNID on that system (required to go online for many things or to download titles from the eshop) you would HAVE to format the system which would delete the games.