Use the Ultimate GBA VC Injector for 3DS https://gbatemp.net/threads/release-ultimate-gba-vc-injector-for-3ds.438057/ to inject gbagi roms and create cia files for 3ds out of it, to allow saving use SRAM (Step1) and SRAM Patch (Step4)  
Use the Ultimate GBA VC Injector for 3DS
https://gbatemp.net/threads/release-ultimate-gba-vc-injector-for-3ds.438057/
to inject gbagi roms and create cia files for 3ds out of it,
to allow saving use SRAM (Step1) and SRAM Patch (Step4)