Probably one is *.sav and the other *.srmHi. I started Zelda Minish Cap on my Switch with RetroArch using the mGBA core and then I switched to using VBA Next. When I wanted to transfer my savegame to my PC, the only recognized savegame was the one I started on mGBA. What should I do to ensure that the VBA Next savegame is the one recognized?
Just take the one you want and rename it.