PSSE is a windows program, so keep it on your computer.
https://smealum.github.io/3ds/ --> Follow instructions here to "install" TubeHax. This will allow you to use the homebrew menu. Ninjhax/ironhax are also alternatives if you own either a copy of Cubic Ninja or if you had downloaded Ironfall before it was removed from eshop.
https://gbatemp.net/threads/tutorial-savedatafiler-ninjhax-pokémon-shuffle-saveedit.393568/ --> You'll need this homebrew on your SD card. Download the archive on first post and extract it at the root of your SD card. It should add a folder inside your "3ds" folder (this "3ds" folder is where you need to put homebrews).
https://gbatemp.net/threads/tutorial-savedatafiler-ninjhax-pokémon-shuffle-saveedit.393568/ --> This tutorial explains how to use SDM. Launch the homebrew menu, then SDM, then select shuffle using Dleft/Dright. After the glitchy screen, you'll have 3 choices : A to backup save, B to import it or X to quit.
Press A to backup your save (It will go in \Savedata Backup\savedata.bin on your SD card). Open your SD card on your computer and edit your file with PSSE. Put the edited file back at the same place and launch everything again, except this time you'll press B to import your new save. Quit (X) then quit the homebrew launcher (Start > A) then launch your game and TADAA !
Pro-tip 1 : NEVER EVER Launch shuffle between the moment you did your backup and the moment you import it back. You can only import in your game the latest save, so if you launch it it will create a new save and tell you the game is corrupt when trying to import the old one. Always make a backup of your backup before editing it, and if you ever encounter this problem you'll be able to restore it using this link :
https://gbatemp.net/threads/antisav...value-updater-ps-acnl-prw-ssb-xy-oras.396644/
Pro-tip 2 : If you do this a lot, you'll have to eject your SD card from your console a lot. Especially if you own a new3DS, I'd suggest you use either Nintendo's "SD card management" (it's in the console's parameters) or the homebrew "FTBRONY" (it's included in the "starter kit" you'll find on hte first link).
You'll be guided by your console for the first one (if windows doesn't see your console, type \\<name you gave to your console> in the adress bar of any windows explorer window).
For FTBRONY, just launch it and you'll see and IP adress and a port on the top of your scrren : type "ftp://<ip adress>:<port number>" in the adress bar of any windows explorer window (to quit the homebrew, press B and close the corresponding window on your computer, you'll be told to press B again to quit. If that doesn't work, open the window again and try accessing folders until it tells you it disconnected).
You must have done something wrong, make sure you follow the instructions I just wrote.
https://gbatemp.net/threads/svdt-save-data-explorer-manager.396562/ --> SDM only extracts blank files on my console and fails to import them back correctly too, so if still doesn't work you can try svdt instead. It has more functionnalities than SDM but is a bit more complicated to handle, so you should probably read everything you'll see on screen to understand but it works like a charm =)