You may still want to get the new download for the 'puter (PCM). There may be a change in the way it controls the motor such as a milasecond change in engagment timing or a wait command that holds enagement until other readings occur with conditions that will prolong the life of the new encoder motor.
Also a new download may have other fixes included, kinda like updating the Windows on your PC. Like all software and firmware, there's always room for improvement. I'd go for it if the service bulletin says to.