[defilade]

I just went through this as well. My car started out with an SB100 exemption and then left CA for two years before I brought it back. When I submitted my registration paperwork to the DMV, they accepted my paperwork and fee payment, gave me an incomplete registration, and sent me to the 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.

That makes it sound a big more straightforward than it actually was. Apparently this is a rare enough case that the procedures aren't documented. All along the way, no one had any idea what the next step was. They'd just say, "let's submit it and see what happens." But it worked out in the end.