Clone and Repro Cart Problems
Problems with carts without a battery pre-installed
If your cart looks like this, if your re-write the rom file and try to save it will appear to have worked but once you power off, your save will be lost.
How it works
The way this cart functions is the rom is modified to write the save back to the flash chip when you save your game. When the game starts, the opposite occurs, the game extracts your save from the flash chip and puts it back on the SRAM so to the game it appears like everything is normal.
How can I extract my save file
Since the rom has been modified, all you need to do is dump the rom and run it in an emulator and your save file will be created. You will not be able to save again and if you re-load the rom in the emulator, your .sav file will be over written to the original save that is in the rom.
How to resolve the issue
You will need to install a battery or patch the rom you flash to also perform the above technique. At this time there are no programs that can automatically do that for you.