For some of you having problems replacing an edited .sav file may be the way the cart saves the file.
The ds-xtreme for example saves the .sav file from the eprom after the machine is shut of then turned back on and started.
Just do this.

Save your game.
Turn off the ds
Turn on the ds and start the os.
Let it save the eprom.
Turn off again.
Now replace the edited .sav file.
Turn on the ds and start the os (it won´t save the eprom this time overwriting the edited one)
Load the game and enjoy.