WARNING: GodMode9 added a native save dumping and injecting tool that works way better than AGBSave9, you can download it here. Here's how to use it.
I'll be keeping this guide around for historical purposes, but you should use GodMode9 instead.

​

Spoiler: Depreciated tutorial here

Dumping GBA VC saves:​

What you will need:

• AGBSave9 v.1.0 "EEPROM support" (A9LH-compatible version here)

1) Run the game that you want to dump the save and close it.
2) Load AGBSave9 from sysNAND 9.2/A9LH and select "Save Dump".
3) This should give you a screen with this info:

• Title ID: xxxxxxxx
• Use save type 0/1/2: SRAM/Flash/EEPROM
• Creating agb_dump.sav ...

4) Write down the Title ID and Save Type, you'll need it if you want to inject the save back later.
5) Plug your SD card into your computer and copy the agb_dump.sav on the root of the SD to somewhere safe, this is your save file.

Injecting saves into the GBA VC:​

What you will need:

• The "agb_inject" folder from AGBSave9 from v1.0 "EEPROM support"
• This modified "gen_run.py" (Note: The gen_run.py included with AGBSave9 1.0 isn't working properly)
• Python 3

1) Install Python 3, else you won't be able to run the gen_run.py.
2) Copy your save file into the agb_inject folder.
3) Run gen_run.py and follow the on screen instructions, this should generate a .cia file inside the agb_inject folder.

4) Copy the output CIA file to your 3DS' SD card.
5) Install it on sysNAND using your favorite CIA installer, I recommend FBI. (if it asks to overwrite the previous install, allow it.)
If you only have them on sysNAND:
6a) Run the CIA that you just installed. (It should show up as Fire Emblem on the top screen)
If you have them on both NANDs:
6b) Run the game that you want to inject the save on emuNAND.
7) When "AGB_FIRM save injector" appears, turn off your 3DS.
8) Insert your SD card on your computer and go to "/Nintendo3DS/(YourSysNANDHere)/(RandomStuff)/title/00040000/(TitleID)/" and copy the data folder.
9) Reinstall the game that you want to inject the save on sysNAND. (if it asks to overwrite the previous install, allow it.)
10) Reinsert the SD card on your computer and copy the data folder back into "/Nintendo3DS/(YourSysNANDHere)/(RandomStuff)/title/00040000/(TitleID)/"
11) Run the game, if everything worked properly, your injected save should appear on the game.

Credits:
@alex34567 7 for AGBSave9.
@redunka for the fixed "gen_run.py".
@Frelia a for the A9LH-compatible version.

 

[MushGuy]

The rom is ripped from my personal cartridge using Gba Backup Tool on my dstwo in a DSlite, also is the save.
The weird thing is that on VBA it says that the battery has run dry but no error about saves, but on GBA VC it says as written above.
Is not a big problem since it keeps saving normally, but read everytime that messag is so annying ...
I also tried to do the whole save thing trough agb_inject but it's the same ...

I think the problem is that your ROM needs to be patched form 128KB to 64KB. You can get the necessary patches here, and inject your ROM again to be able to save. But I suppose you patched it already, since you say it keeps saving normally, but if you didn't, then use the patch. As for VBA, are RTC and 128KB save turned on?

 

[Yamanoko]

I think the problem is that your ROM needs to be patched form 128KB to 64KB. You can get the necessary patches here, and inject your ROM again to be able to save. But I suppose you patched it already, since you say it keeps saving normally, but if you didn't, then use the patch. As for VBA, are RTC and 128KB save turned on?

The only thing i did is the hex patch mentioned in another thread on this forum, otherwise the game stops at a Blank Screen after GBA logo.

 

[MushGuy]

The only thing i did is the hex patch mentioned in another thread on this forum, otherwise the game stops at a Blank Screen after GBA logo.

OK, try the patches that I mentioned before with a clean ROM, and tell me what happens.

 

[Yamanoko]

OK, try the patches that I mentioned before with a clean ROM, and tell me what happens.

I read that the patches are for the USA version only and my game is Italian :/

 

[MushGuy]

Oh, in that case, you could try asking if porting these patches to other regions is possible. And you're talking about this hex editing thread, is that right? Either way, try hex editing again. If it still doesn't work, try asking there for help.

 

[cuchillas]

which is the correct procedure to dump and inject gba save data with decript9?

 

[twosidea]

Did all the steps accordingly, booted up GBA VC and there's no save file to load. I attached an image of the process of making the save-cia file. One thing to note is that the original GBA save data is only 8KB big and is originally from a US ROM. However, the VC I wanted to inject into is EUR region.

EDIT: Apparently the save file that the VC needed was a SRAM type. Seems to be a bug amongst a few EEPROM games. Fixed and finally got the save loaded!

 

[AvatarMew]

The save file I dumped is 8 kb... Is there anything I can do?

 

[matpower]

The save file I dumped is 8 kb... Is there anything I can do?

Did you dump it with AGBSave or Decrypt9?

 

[AvatarMew]

Did you dump it with AGBSave or Decrypt9?

AGBsave since I can't use Decrypt9 as I don't have the Slot0x24keyY file

 

[matpower]

AGBsave since I can't use Decrypt9 as I don't have the Slot0x24keyY file

You can find it in Plailect's guide. It's the aesdbkey(Basically, all the Slot keys in a single file) or something. Give it a try with Decrypt9, if it still doesn't work, tell me.

 

[AvatarMew]

You can find it in Plailect's guide. It's the aesdbkey(Basically, all the Slot keys in a single file) or something. Give it a try with Decrypt9, if it still doesn't work, tell me.

I've tried Decrypt9. I can inject the save but it doesn't work.

 

[matpower]

I've tried Decrypt9. I can inject the save but it doesn't work.

Are you injecting the 8kb save that you previously dumped?

 

[AvatarMew]

Are you injecting the 8kb save that you previously dumped?

Yes.

 

[matpower]

Yes.

Hmm, I thought you were going to redump it with Decrypt9. It looks like it's corrupted or something? Check it out in an emulator too.

 

[AvatarMew]

Hmm, I thought you were going to redump it with Decrypt9. It looks like it's corrupted or something? Check it out in an emulator too.

It works in an emulator fine.

 

[matpower]

It works in an emulator fine.

Hmm, in which game are you trying to inject that save btw?

 

[AvatarMew]

Hmm, in which game are you trying to inject that save btw?

Legacy of Goku 2.

 

[matpower]

Legacy of Goku 2.

Hmm, I wonder... did you patch the game? IIRC it uses EEPROM which has some issues in certain emulators. I think some people patched it as SRAM. Try exporting the save in the emulator in a different type and see if it works.

 

[franchoise2]

i have that, and that's the setup gives me that error

do u know how to upload a gba gamesave and put it on your 3ds and have all the stages unlocked without playing thought the game???