So I have AC downloaded on the 3ds since it's the collectors edition. If I wipe my info, I can sell it and the game will still be on it right? I mean, it obviously wasn't linked to me when I bought it.
That would bind it to your NNID, so I don't think so. I think if you just removed all your personal data, then selected to recreate the town but didn't make a new one, it'd be about as good as new.
The game is already pre-downloaded on the DS. Your data is on the SD card. Usually, transferring the data to a new copy of ACNL would most likely cause the data to be formatted. I wouldn't try it in my opinion. Bu of course, it is up to you!
If you're certain of selling it then just wipe it and see. If it's not on there then reduce the price you were planning to sell it for and make sure the buyer understands that the game won't be on it.