This is a step-by-step guide on how to modify your save file (for extra jewels, coins, missed pokèmons etc) with a Gateway.
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Prerequisites:

– .3ds file Pokèmon Shuffle placed on your Gateway mSD Card
– 3DS booted into Gateway mode (emuNAND not needed)
– SaveDataFiler CIA installed via BigBlueMenu
– Pokemon Shuffle Save Editor (PSSE) by SciresM (github) (PSSE.v1.0.zip mirrors)

Part 1 - Preparing your save for exportation
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a) Connect your SD Card (internal 3DS card) to your PC
b) Make a backup of your Pokèmon Shuffle .sav (0004000000141000.sav), save it as e.g OLD_0004000000141000.sav
c) Rename Pokèmon Shuffle .sav to the general save ID, so the final filename becomes 000400000FF40A00.sav
d) Now put the SD Card back into your 3DS, boot into Gateway mode, load up Pokèmon Shuffle via the Gateway SELECT menu (don’t open it), then enter SaveDataFiler.

Learn more about why you need to mess with the general save ID (and learn more about exporting/importing GW Card1 save files) in this thread by liomajor.

Part 2 - Exporting your save to get to the .bin
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a) In SaveDataFiler, navigate to the “User” tab. If you’re seeing «CTR Card — broken —» now, please go back to Part 1 and follow each steps carefully.
b) Highlight «CTR Card» and press Y to export the save file to your SD Card.
c) Connect the SD Card back into your computer, navigate to filer/UserSaveData/xxx/00001410/ and voilà, here’s your savegame.bin

Part 3 - The fun part aka f*ck the «F2P» model
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a) Modify the .bin to your hearts content using PSSE

b) Click «Save savedata.bin» and ovewrite the savedata.bin you opened
c) Now move this savedata.bin back on to your SD Card in the exact same folder, replacing the original file

e) Eject your SD card and plug it back into your 3DS, boot up in Gateway mode, load Pokèmon Shuffle (don’t start it) and enter SaveDataFiler again

Part 4 - Importing our hacked file & encrypting it back into the .sav format
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Back in SaveDataFiler

a) Go to the “User” tab, highlight “CTR Card” and press R+X. This deletes the secure values, and is a very important step in preventing data corruption. Don’t skip this.
b) In SaveDataFiler, go to the “SD” tab and highlight the correct title id (in our case 00001410)
c) Press A (L+A) to import the save
d) Almost there! Now plug the SD Card back into the computer and swap the original Shuffle save file with the general save ID file (i.e delete your original Shuffle save and rename the general save id to 0004000000141000.sav)
e) Finally plug the SD card back into your 3DS

Congratulations! It’s time to boot up Pokèmon Shuffle and enjoy your freedom (one million jewels!)
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tl;dr

1 - Export .bin with SaveDataFiler (but to avoid CTR Card broken error, rename pokemon shuffle save id to general save id)
2 - Hack .bin
3 - Reimport .bin
4 - Rename general save id (which is now based upon your newly imported bin) back to the shuffle save id


notes:
1) you can safely delete secure value in savedatafiler (and should do so before reimporting to avoid data corruption)
2) shuffle save id: 0004000000141000
3) general save id: 000400000FF40A00
4) PSSE is Windows only. If using a Mac use Windows via VirtualBox and set up a shared network folder (as done in this tutorial)

 

[Cloudisfast]

Good tutorial.

I'm using Save Manager, and every time I export my save file, it's never the same as what's actually saved within the game. Any idea why this is happening?

EDIT: Don't worry, turns out I have to delete the extracted save, back it up, and repeat multiple times. Seems to be a Save Manager bug.

 

[samiam144]

A quicker method to replace step 1 & 2 would be to use the NTR 3.0 cia + the save manager plugin. No need to remove the SD card so many times (a nightmare for N3DS users, I'd imagine!). You can do multiple games at once without removing the SD card-> renaming-> etc.

 

[heroarc8]

are there any ways how to use it on cia version of the game?

 

[samiam144]

are there any ways how to use it on cia version of the game?

Yes, just use SaveDataFiler