Yeah, I don't know that that'll work.
The only sure way of doing it would be to restore a copy of sysNAND from before you unlinked as suggested above.
If you could restore a sysNAND backup from before you unlinked, all you'd have to do would be to link your existing NNID to your sysNAND to be able to use it on both. In addition to that, when you connected to the eShop from sysNAND, all of the titles you installed on emuNAND would appear on the sysNAND homescreen.
Oh well, more fool you for not keeping a backup of your sysNAND before creating your emuNAND. At this stage though, your options are few; you can either create emuNAND from scratch and lose all your data, or you can install everything from .cia files from here on out.