If you REALLY want the update there are two options.
One: RUU back to stock, accept the OTA, then re-root.
Two: Ignore it, S-Off, and follow the thread saying how to turn your phone into an Evo 3D.
S-Off is not too hard, the timing is the worst part. I finally did it, and boy. I'm glad I did. AOSP/AOKP Roms are phenomenal. That and I have a better radio/PRI now