But, if you talk about the boot flash. You to reboot with the console port. Keep in mind, you have to download a new FortiOS inside your Fortigate after format. The device will not boot after. AND, you will loose all you fortigate's configuration. Be sure to have the FortiOS file and a TFTP server ready before formating a device.
------------ Console logs ------------
Please stand by while rebooting the system. Restarting system.
FortiGate-90D (20:14-02.28.2014) Ver:04000020 Serial number: FGT90D3XXXXXXXXX CPU(01): 900MHz Total RAM: 2GB Initializing boot device... Initializing MAC... nplite#0 Please wait for OS to boot, or press any key to display configuration menu..
: Configure TFTP parameters. : Review TFTP parameters. : Initiate TFTP firmware transfer. : Format boot device.: System information. : Boot with backup firmware and set as default. : Quit menu and continue to boot. : Display this list of options.