AFAIK 00040000 is the folder Nintendo uses for Pokemon Y. In subfolder 00057700, 00055e00 and 00051700 there are 3 x 00000001.sav files of different sizes (512 kb, 1,024 kb, and 128 kb).
I added a (1) (2) (3) to show the respective files (as they have the same name) and are here in the .zip file.