Gateway creates such files for every game, but the REAL .sav is stored within the game.
To extract it, you have to use SaveDataFiler with the Pokemon ROM loaded in the card (selecting it through Multi-rom menu).
Then go to SaveDataFiler card tab and extract the .sav from there.
You can verify which .sav is the correct one by loading it with PK Hex and checking if all your currently caught Pokemon are there.
For me, it makes a sav file for every game including Card2 games and even installed channels.
This is how the SaveDataFiler workaround for card1 games works, by renaming the .sav for your chosen game to the titleID of SDF so that the GW is tricked into loading that save onto the cart when you launch SDF.