flasher-3.5 -F RX-51_2009SE_20.2010.36-2.002_PR_COMBINED_002_ARM.bin -f
The above cmd flashes the softwares installed and rootfs of ur mob but keeps all ur files, pics, videos data, phone book, sms etc intact.

flasher-3.5 -F RX-51_2009SE_10.2010.13-2.VANILLA_PR_EMMC_MR0_ARM.bin -f -R
This cmd flashes the phone completely. It will be as new as u brought it.

More over, -f means flashing only
-R means reboot after flashing.