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.
FOLLOW ME!!!! RANGERS LEAD THE WAY!!!!