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I would like to have start a game over, but do not want to erase my current progress in case I have second thoughts and want to go back. I could create a 2nd account & NNID on my Wii U, but if my 2nd save ends up being where I do the big 100% completion or another major achievement, I'd rather it were on my main account (mainly for the Miiverse bragging rights!)

My Wii U is connected to an external hard drive. I can copy save files to either the system memory or a second external hard drive. Is it possible to [ab]use this to have multiple save files for a single game under a single user ID (where the game itself does not offer multiple saves)? Theoretically it should be like the old swap-two-variables programming problem:

MAIN: External (main) hard drive   EXT2: External (2nd) hard drive   SYS: System Memory   

1) Copy save1 on MAIN to EXT2
2) Erase MAIN data
3) Start new game (save2 created on MAIN)
-- To swap back: --
4) Copy save2 on MAIN to SYS
5) Copy save1 on EXT2 to MAIN
-- To swap back again: --
6) Copy save1 from MAIN to EXT2
7) Copy save2 from SYS to MAIN

Theoretically it's possible to maintain two separate save files under one account like this. However, does the Wii U do anything to prevent me from doing this? I know this was not doable on the 3DS - a friend of mine copied his Pokémon data (this was before the firmware Backup Save option for digital games), erased the original and started a new game, and was unable to restore the original data later - the system simply wouldn't read it.

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The Wii U Data Management feature in the System Settings allows for this. The steps you listed are exactly how you would want to go about. It is possible however that you may want to disconnect the secondary hard drive after using it if you run into any difficulties. Nintendo states on their support pages how it determines which location becomes the default location for the save file and it does not sound like it is expecting there to be two drives connected by the end of the process. It may work anyways, but it is something to keep in mind in case it doesn't.

If you copy save data from your system memory to a USB storage device, the USB storage device will become the default location for all new saves for that title.

If you copy save data from a USB storage device to system memory, the USB storage device data will remain the default location and all new saves will continue to be saved to the USB storage device. This cannot be changed unless the USB storage device is removed.

If you copy data between two USB storage devices, whichever device remains connected to the Wii U after the transfer will become the default location for all new saves.

Official Nintendo Support Links

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