I personally don't recommend update a rooted phone, from 2ch, some of SH-02E(or SH-06E) rooted phones has been brick or cannot be root again after specified version. And that was a bit reason that the author of the root program writing a loop before booting into OS(for writing info and can be connected by adb command).
I also want to upgrade my SH-06E this time due to HDR video, but I will rollback to non-root phone.
I think it's modify the ROM area but restore by Recovery Area, so the loop kept before booting OS is used to prevent the System folder from becoming readonly.
I don't try that before, and I might have no time to restore then rent a docomo card, so might not do update this time.
btw, a few ppl have successfully crackked SH-06E sim lock, but need to know how to use compile tools. I will not provide any link, just google and try it your own risk.
I'll try it on my new coming 203sh coz it's really cheap at amazon, it worth the price even as a walkman and a waterproof camera.