Sorry but please don't misunderstand I haven't configured anything at all. This is an old save file that alredy had that size and I don't know why nor how to fix it. The game still play like normal in the emulator.
I have this same problem with Pokemon Black with a 1mb sav file. However the most recent version of Desmume still give me a file that is too big to be read or rather it doesn't change at all (I definitely save it properly).
Pokemonblack.dsv