Gino, Questions is what the forum is here for
The firmware is stored in a locked section of memory so using the disk tool to repartition and then formating will not erase your firmware. If there are any files on your player that you want to keep though you should remove them as they will be erased.
That is right the s1fwx will extract the firmware but it will not repair it so the backup will not load to your player. The 9.0.XX series of firmware is for newer chipsets the ATJ2097 and the CTW500, these chips are different than the more common chips that s1fwx supports.