I don't think it works that way. I don't think Nintendo reps can see what's on your 3DS. I would guess that the 3DS sends data to the linked account and if there is none, no data will be sent. If they make the 3DS send data like this retroactively upon linking, one could change the account multiple times and register the game on different accounts. Of course, there are also solutions to this but we are talking about Nintendo here, I would always check if everything is in order beforehand. Complex online infrastructure just isn't their forte.
Ongoing bet with think-man: He wins if MH4 releases in any shape or form on PSV in 2013, I win if it doesn't.