This Article, How to transferring Save to 3DS will show you the way to transfer save file from GB/GBC/GBA to Nintendo 3DS. It’s from Pokemon Crystal Clear documentations but you can apply it on all GB/GBC/GBA ROM you can play on Nintendo 3DS. If you don’t know Pokemon Crystal Clear, You can read Pokemon Crystal Clear post to know more.
Starting the tutorial
Grab your .sav file. In BGB the proper file is generated automatically, and in VBA-M you simply choose Export > Battery File.
Rename the .sav to sav.dat.
Using a hex editor, remove the last two lines of data from the .dat.
On your 3DS, export your save data. We used JKSM!
On a 3DS with Crystal Clear installed and using JKSM, navigate to Crystal Clear and select Export Save.
You will be prompted to create a folder – remember the name!
Turn off your 3DS and put its SD card into your computer (or use an FTP client).
Navigate to the folder made with JKSM and replace that sav.dat in that folder with the one you made. Note that the folder in the root of your SD will be JKSV, not JKSM.
Back on your 3DS, launch JKSM and import the save data!
Note: Any dumped 3DS save renamed with a .sav file extension will work in your emulator!
I hope after you read How to transferring Save to 3DS article, you can know how to transfer save file. So if you have any problem when you convert gba to cia, you can read Fix all save problems for Pokémon games (VC GBA).