Sorry i think i was being confusing. I want to reflash my device not just the rootfs but the whole FIASCO but not the emmc. I've downloaded flasher 3.5 and plan to use the command:

sudo /usr/bin/flasher-3.5 -F RX-51_2009SE_20.2010.36-2_PR_COMBINED_MR0_ARM.bin -f -R

My understanding is that this preserves my data and will let me get into the system. Is this correct? If not please let me know as I plan to do this asap!