.bak files are just backups that are created when you use HxD (other programs might create them too, but I know for sure HxD does). Their filename should be in the form of “filename.gba.bak” if it’s a backup of a GBA ROM. If you remove the .bak extension, it becomes a .gba and can be run in an emulator.
If the sizes are different, compare the date that each file was last modified. The .bak is likely just an older version of the ROM.
Save files don’t have anything to do with .baks.
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