This was a while ago, so you might've already done stuff? but those pokemon are probably going to be deleted.
Strictly speaking, the NNI isn't the kind of thing you putz around with. It's a dangerous thing to delete out of nowhere.
Why? Because the NNI is connected to the currency in your account. It is what allows you to buy things. And the money doesn't transfer between regions (you can't change dollars to yen) so you'd lose that.
In that link before, there was something said that could be considered pretty scary. Basically (emphasis mine):
Can I register the same Nintendo Network ID on more than one Nintendo 3DS system?
No, this is not possible. Your Nintendo Network ID is tied to your software and/or additional content you have purchased and downloaded. As the rights of usage for software you have purchased apply only to a single Nintendo 3DS family system, you can only register your Nintendo Network ID on one system.
The bolded statement makes people think they cannot ever change their NNI. But that's not the case because you can add a new NNI:
What is retained:
All game licenses purchased prior to linking a Nintendo Network ID.
Funds added prior to linking a Nintendo Network ID. (See "What is NOT retained" for restrictions.)
Additionally, if a Nintendo Network ID is linked to both a Wii U and a Nintendo 3DS, the Nintendo eShop balance is consolidated and shared between them.
All free software demos downloaded prior to linking a Nintendo Network ID.
As far as deleting goes, though... completely different story. you can keep your stuff if you format your system memory. That's because:
Deleting a Nintendo Network ID will also delete the following information associated to the account: Nintendo eShop activity and balance, Friend List, Miiverse activity, and registered e-mail address.
Now! I know what you're thinking: These are prior purchases, they don't have anything to do with my NNI, blah blah blah," but, here's the thing-- deleting your NNI has a process to it, and THIS is a part of the process:
Agree to the following points:
The Nintendo eShop and all associated purchases will be deleted, and cannot be downloaded. This applies to purchases made with this Nintendo Network ID both on the Wii U and Nintendo 3DS.
Any remaining balance in the Nintendo eShop account will be deleted and cannot be recovered or refunded. This applies to funds added to this Nintendo Network ID both on the Wii U and Nintendo 3DS.
The Friends List associated to this Nintendo Network ID will be deleted.
Any posts and comments made on Miiverse will be deleted.
Long story short: If you do it, do it carefully.
No, you will lose the games or be forced to transfer them to another system.
Games are tied to both the system and the NNID. The 3DS only supports one NNID to be linked to it at a time, unlike the Wii U which allows 12. The only way to unlink a NNID from a 3DS outside of a system transfer is to format the system. If you link a new NNID after that, then you will not be able to redownload the games.
How to Change Nintendo Network ID Information (E-Mail Address, Gender, Region, Etc)
Your best chance is to contact nintendo's support and see if they will help you out.
Best Answer
You can re-download them via the Nintendo Switch eShop.
Follow these steps.
On that page, Click Downloading a game, then I don't see the game on my Nintendo Switch!