first of all. people are not replying properly becauser this question has been askedd million of times. use the search function

secondly if your computer recognises phone in cmd. then flash it. doesnt matter if the battery is less then half

run these commands

cd "%ProgramFiles%\maemo\flasher-3.5"

flasher-3.5 -F RX-51_2009SE_1.2009.42-11_PR_COMBINED_MR0_ARM.bin --flash-only=kernel -f -R

change the bold writing to your file name...

steps
take the battery out. disconnect the phone. open cmd. run those commands. when it says "waiting for suitable device. connect the cable. press U. put the battery in. keep holding the U key until it starts flashing in cmd