I just joined pretendo and installed it on my 3ds via universal updater and launched it in homebrew. When i transferred IDs i made sure to turn on pretendo services instead of nintendo. Afterwards i went into settings and changed nintendo ID fro-m my old one set to the pretendo one. My 3ds system said i wouldnt lose any data but that my new nintendo id(the pretendo) that i would be putting into my system would overwrite my old actual nintendo id. IDK if its bad that i used the same gmail for both of them but thats the case. Anyways, once i overwrited my old nintendo id to my new pretendo one, when i relaunched my 3ds i noticed all the games i reinstalled from eshop dissapeared. I looked into my storage and they were still in my sd card but were greyed out and had an X icon on the corner of the app icon(Pokemon Plata, Pokemon Rumble world, Dragonball, etc.) and i figured maybe its a bug so i deleted it and rechecked the nintendo eshop. Sure enough when i check to reinstall the games didnt appear and there was only 2 games that showed with was tomodachi life demo that i didnt reinstall originally and dragonball extreme butoden which i also didnt reinstall originally before the ID transfer. For some reason the apps i had decided to not reinstall yet were still options to reinstall in eshop but not the games i had deleted. I BELIEVE i deleted the games that didnt work on the pretendo servers and when i switched back to nintendo servers to open eshop they didnt show. So my theory is that i stepped on my own toes by uninstalling in pretendo and then switching to nintendo servers which indefinetly erased the games forever and can only get them from OTHER means instead of deleting them in nintendo servers.
TL;DR: I deleted eshop games while in pretendo servers cuz they dissapeared when i transferred njintedo IDs and switched back to nintendo servers to check eshop to redownload said deleted games to find out that there isnt an option to redownload them
Anyone ever suffered from a similar issue/outcome and resolved it?
i want to say that System Transfers are not supported by Pretendo Network, and you may lose access to your PNID.
attempt to switch back to your NNID to redownload all software you own.
this happened to me, reinstalling helped.
this means you do not own your software.
edit: try contacting nintendo support, actually. not sure how they will help, though.
this is very very wrong. deleting games while in Pretendo Network should never have affect to your online, SEPARATE account, that you aren’t even connected to.
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I realized the cause of the problem. I was looking at a tutorial for installation for Pretendo and people in the comments were saying they lost data for their games and most of the people in that comment replied with to delete your NNID by doing GM99 going into scripts and deleting NNID. I thought i would lose my game data, so blindly, i followed and deleted my NNID before doing the pretendo process.
[Moderator note: redacted section]
Strangely though, even when i deletd my NNID and rebooted the system to do the process, the games were still saved in my sd storage and i was still signed into my old nnid but once i had deleted the overwritten the nnid and deleted the games i cant redownload them anymore. I’ve had no luck trying to log back into my nnid and my memory is very fuzzy so I don’t even remember my username nor nickname of the NNID nor the password. All i know is that i used the same gmail for my PNID and NNID. Thanks for the help anyways i will try to contact nintendo but i fear they will have no interest in the 3ds system 
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I take it that this was a video guide? Never use a video guide, bit late for it now but it seems that the guide you were using had misinformation in it, which is why we do not recommend video guides
Removing your NNID from the console was completely unnecessary as Nimbus switches to a different profile
Unfortunately, we cannot help you with recovering the NNID, as that’s something on Nintendo’s server that we naturally would not have access to. Contacting Nintendo would be your best-bet on trying to recover the account details
I hope you’ll eventually recover your Nintendo Network ID