I don't think its possible to have a working eshop with the same nnid on both the emunand and sysnand. I have two separate accounts, the real one on my emunand and a fake one on the sysnand. So if you relink your real account to your sysnand it may permantly break your emunand, but I'm not entirely sure. I think it would be safer to have them separate. To answer your question formatting will not lose your purchases but you will need to download them again if they were on your sysnand.
Not quite true. My emunand and sysnand are linked to the same NNID account, but they are not linked to each other. I achieved this after manually migrating a movable.sed seed from an old 3DS that used to be bricked. (the guy I sold it to was able to unbrick it and was kind enough to provide a decrypted dump of my emunand). So I did the needed edits to movable.sed and copied it and the data folder linked to it to my 3DS XL's emunand.
This is basically a "manual" system transfer. The only thing that doesn't get transfered are the tickets. But if you have the tickets on the emunand/sysnand you are manually system transferring to, the SD card content will show right up once you finish the process. Do not ever attempt to manually transfer the tickets.db file from a different console to another. It will brick emunand and if you attempt it on sysnand it will brick the console. The file is encrypted using console unique keys and even if it wasn't the tickets stored in them (other then the common tickets used by system titles) are unique per console and you have to go through the system transfer process (or use eShop on new console after you transfer the NNID to it) to move the tickets over.
This allowed me to use all my old games/save games that my bricked 3DS had on my 3DS XL. Because my 3DS XL was linked to the same NNID as the old one (I manually transferred the account by calling Nintendo) I then had that working on emunand. I then took the movable.sed/data pair I used to have on my emunand on 3DS XL and moved that to sysnand.
So they both can access eShop now and because the movable.sed seeds are different, they use different folders on SD card. (thus are unlinked from each other)
Note for those who want to attempt this but have only one 3DS. You can backup emunand, (and the SD folder for it), then use system format while in emunand to unlink. This will allow you to relink NNID to your sysnand (assuming you have a 9.x or higher sysnand with the eShop spoof CIA).
Then simply restore your emunand backup. As long as you didn't change your NNID info like password, they should both be able to use your NNID now.
