Sorry to resurrect an old thread, but I just went through this with a Cobra, and wanted to share my experience for the benefit of others since this post comes up in Google searches.
My car was issued an SB100 exemption when it was built. Some time later, it left CA for a few years before I brought it back. When I submitted my registration paperwork to the DMV, they accepted my paperwork and fee payment, and gave me an incomplete registration. The paperwork did say smog was required, so they told me to make an appointment with a BAR referee to sort out the SB100 issue. I did a phone call with the referee, who requested pics of the SB100 sticker and VIN. He then submitted that info and they put the smog exemption back on my VIN within the DMV system. Went back to the DMV and got my plates and stickers.
So it sounds like the smog exemption does drop off your VIN when the car leaves the state, but the good news is you do not have to start over from scratch with a brand new SB100 application. It appears that proving that you have an SB100 sequence number associated with your VIN is sufficient to renew the exemption.