Does anyone know exactly what the system deletes when it formats the memory, will I lose game saves?
DS and 3DS game data is saved on the game card itself.
eShop titles' save data is on the system, so you will lose that, along with Miis, SpotPass data, StreetPass data, and other personal data.
You can, but you'll have to pay for them again. Formatting basically makes the system brand new and deletes any and all data that it is able to. Your Nintendo 3DS eShop account will be closed, null, and void.
I'm not so sure that you won't be able to redownload the games for free.
I would recommend that you call Nintendo at 1-800-255-3700 to double check prior to formatting.
As for what you lose, the online guide says the following:
The following information will be lost after formatting the system memory:
System Settings data
So game data for game cards such as The Legend of Zelda 3D will remain on the card, as this is not stored on the 3DS.
Yes, the games themselves will be gone, but the question is whether you can then redownload them for free or not.
The answer to that depends on how the eShop identifies the 3DS, which we do not know. Some identification methods (such as the friend code) change after a format. Some (such as the WiFi antenna's MAC address) stay the same.
Yes. One of the primary reasons that a user might want to format the memory is so that he or she can sell it.
Thus performing a format will wipe personal data and ready the unit for use by another person.
Might I ask why you want to format the memory?
Well I sent my 3DS in for repairs and they fixed the problem it had, but they seemed to have disconnected the battery during the repair process. That of course means that streetpass doesn't work properly. So I called Nintendo about it, and they that I could reformat the memory to fix the streetpass problem.
wierd that the problem would arise after a repair from nintendo
most game data is stored on the sd card (ex. Pokedex 3D), so as long as you take out the sd card during the format, it should be fine
also, if i have this right, you can delink your club nintendo account from the shop, then relink them to get your download history back and be able to redownload everything
EDIT: NO DONT LISTEN TO ME LOL look here
You will not be able to re-download your games for free. When you go into "Format System Memory" it says:
"Software saved to an SD Card will no longer be usable."
This means that your licenses for your downloaded software are deleted, and you will not be able to download them for free. I suggest you call Nintendo again. There's got to be a better fix than formatting your system memory.
I was mistaken when I said your DSiWare cannot be restored. A system format does not delete your DSiShop account, as NOA_TECH_MIKA mentioned here: http://techforums.nintendo.com/message/49142#49142.
This means that after a system Format, you will be able to redownload (for free) any games you previously purchased from the DSiShop. The format will delete the games that are stored in system memory, but you can redownload them for free.
eShop purchases are tied to the Nintendo Network ID. If you delete the NNID, you will permanently lose the account and all the games downloaded from the eShop with that account. I'm not sure why you think you need to remove the NNID in the first place though.