Save editing in Fates is actually pretty easy if you have the right tools in front of you. I wanted to make a basic guide that works with people who are unwilling to use CFW (to avoid getting console banned from the 3DS's online features) and those who honestly have no idea what they're doing. This guide will work for both a physical and digital copy of Fates, but only for Fates. How many paths you have is irrelevant, but I recommend clearing at the very least to Chapter 6 on the file you'd like to futz with.
This is the bare minimum required to start editing:
You must have access to Homebrew on your 3DS. It is necessary to extract your save file. Learn how here: https://3ds.guide/
To actually perform the extraction, you need JK's Save Manager. It's very easy to use, and there will be instructions in the guide. Get it here: https://github.com/J-D-K/JKSM/releases
Lastly, you'll need a fantastic program called FEFTwiddler. This is what we'll be using for the actual futzing. I should clarify that you run this on your computer. Putting it on your 3DS SD card does nothing but occupy some space. Link: https://gbatemp.net/threads/feftwiddler-fire-emblem-fates-save-editor.422439/
Okay, you've got all that? Great.
How to extract your save:
Go to Homebrew with your launcher. I use soundhax. If you have set it up correctly and scroll down, you'll see JK's Save Manager. After selecting it, it will prompt you to pick a title. If you've got the physical version, it'll pop up as the first choice. For download, keep hitting right on the D-Pad until you find it, and select it.
You'll be shown Save Data and Extra Data on the menu. Which one to select depends on where you saved the file you wanna mess with. If you only have one path purchased, you'll have 3 save slots. These are all under Save Data. You get 3 more save slots with the purchase of the opposite path, and another 3 with Revelation. These extra 6 are just that; extra. they're stored in your Extra Data. Select the option that corresponds with the location of the save you want to edit.
The first option under both of these says "Extract Save/Extra Data" This is what you want. If you've never done this, the only option is "New". Name your folder whatever you want (I usually do the date of extraction), and press A to finish entering the name. It will then extract all of your data. Don't worry, this alone does not affect your game in any way. Everything is still there as you left it. After this is done, turn your 3DS off and take out the SD Card after it's all the way off. Pop it into your computer and open up the JKSV folder. Go to either Saves or ExtData and open the Fates folder. Look, a crapton of files you probably don't know what to do with!
Congrats, you're ready to start editing!
How to use FEFTwiddler:
You'll see your save file right at the top. If you saved your game in the top of the first column, it'll be "Chapter0". For example, my Chapter0 is Halea, and, as you can see in the image, it's the first save in my extra data saves. Ebby would be "Chapter1", Ethan "Chapter2", and so on. Open Twiddler and click "File", then "Open File". Then just open the save file you wanna mess with, and go nuts!
Some things you can do:
You can change the class of any character, revive Scarlet in Revelation, let every character learn any skill (including class-exclusives, enemy/NPC exclusives, and Corrin-exclusives), S rank all of their weapon ranks, give them capped stats and Movement, Dragon Blood, and the ability to Heart Seal into DLC classes like Witch, Ballistician, Great Lord, Grandmaster, Lodestar, etc. It's crazy how much power you're given. Yes, you can make Gunter a Maid. It makes Rev's later chapters downright nightmarish, but you can do it. Not to mention that there are a ton of people on GBAtemp with crazy hacks you can insert into your game using Twiddler.
Alright, let's get my changes into my game:
After you've saved your changes, pop your SD card back into your 3DS and boot up Homebrew again. Go to Save Manager, then to Save or Extra. Press Import Save/Extra Data, and select the folder you've been using. Import this, and all of your changes should be in your game once you load it up!
If you want to make a big change, like hitting the big ? button, or trying to unplay chapters, I suggest making a backup of your pre-big change save, just in case it doesn't do what you expected.
And that's it! I hope this helped you! Feel free to ask questions, but please keep in mind that I may not be able to answer them. See ya!