The RUU resets everything in bootloader/recovery.So after you have acheived s-off, when you run the RUU it still think's security is active and releases the watermark and flags. This will also keep super CID as with no security = no change back. I figured this out building things for the evo 4g way way back.I was surprised to it reposted several times everywhere. Some have claimed no need to relock before RUU but i dont see that as possible,since RUU checks bootloader. <<<<<<<<<<<<-PLEASE READ OP>>>>>>>>>> liamstears has the exact method perfectly laid out for you. DO NOT BYPASS/ALTER ANY STEPS. READ then READ again,you will need to re-install recovery and custom rom or root.Done correctly nothing will happen but you doing the happy dance.
"Do you know the terror of he who falls asleep, to the very toes he trembles, because the ground gives way under him, and the dream begins....."
This might be your dream,but it's my RULES!