If it's a pokemon game chances are your vba defaults to save size of 128kb. load up your game on vba then goto: options->emulator->savetype, then change the save to 64kb flash.
save your game on vba then try injecting the new save file.
https://gbatemp.net/threads/fixes-for-all-gba-pokemons-save-issue-with-agb_firm.390508/
follow this guide
Note: it will say your files are corrupt and deleted after the title screen but it doesn't actually delete the save. just scroll through the text to reach the save.
1. check if you have the aeskeydb.bin from part 3 of Plailect's guide in the root of you SD card or your files9 folder
2. copy the save file you wish to inject in to files9 folder and name it gbavc.sav
2. start the gba game that you wish to inject the save into
3. wait until the game reaches the...
Im' pretty sure both system needs to be on the same firmware to enable system transfer. seeing as you have OoThax you can upgrade n3ds to 11.1 and system transfer, then use OoThax to downgrade
I found this save file:
all character unlocked
all character lv 99
all gold skulltula
all heart container/pieces
10 my faeries/ two styles for each element
all my fairy costume
all my fairy consumables
all weapon unlocked with 5 star 8 slot lv4 weapon for each character