Here's a quick tutorial if you ever get the savedata is corrupted error message
1. Either boot up into HBL or execute BrowserHax (or however you get into HBL)
2. Make sure you have svdt in the 3ds folder on SD Card
3. Run svdt and you should get a prompt asking if you want to either enable or disable automatic secure value rewriting on restore (Press A to enable it)
4. Open the Pok+mon Shuffle folder and press X to delete the existing folders and bin file under SD Data
5. Highlight the bin file under save data and press Y to copy it over to SD Data
6. Press Start to exit to HBL and Start to boot into Home Menu; then turn off your 3DS
7. Take out the SD Card and put it in your computer, then copy the bin file from the svdt folder on SD Card over to any folder on your computer (I created a folder named Pokemon Shuffle Save Data and also timestamped subfolders)
8. Open PSSE and Open your savedata.bin file that you copied over from the SD Card
9. Edit whatever you want, etc.
10. Now it's time to Save the edited savedata.bin file (when selecting where to save it, just overwrite the existing bin file)
11. Now, copy the "new" savedata.bin file over onto the bin file in the Pok+mon Shuffle folder within svdt's folder on your SD Card
12. Take out the SD Card and put it back in your 3DS
13. Get back into HBL and run svdt
14. Refer to Step 3
15. Open the svdt folder and then open the Pok+mon Shuffle Folder
16. You'll notice the bin file we copied earlier as well as a timestamped folder; ignore the folder and highlight the bin file
17. Press Y to copy it over onto save data, then press Select to overwrite it
18. Reboot into Home Menu and run Pokemon Shuffle...and now you should see the changes you made in PSSE
I do this everytime I want to make changes to the savedata and have NEVER gotten the corrupted error message I keep seeing posts about on forums. As long as follow these steps, you too shall be able to play Pokemon Shuffle corrupted error message free. Let me know if it works for you (which it should haha) and Happy Shuffling!