Attempting to restore Edited saves changes file size

[Djarcn]

I backup the saves, edit them with pokegen, then resave them onto the sd card
when i put them on the SD they are the correct size(1024kb) when i insert the card into my 3ds and attempt to restore the modified saves it say incorrect file size and when i put the sd card back into my computer there are now 2 files that are 512kb, a .sav and a .sav.bak
what cause this? am i doing something wrong?

[Djarcn]

so i figured out that when i try to restore the edited saves, instead of restoring them, TWL decrypts and rejects them.... they arent decrypted when i insert the SD card into the 3ds, this happens on the 3ds and the only thing i do is try to restore then turn it off

[ghost]

You mentioned PokéGen. Gen. IV and V Pokémon games use 512KB save files.

What save file size does TWLSaveTool report? Does it actually give you 1MB save files when you back up from the cart?