I believe they got a permit after the last cutoff date, they'll show up in the next one most likely.
Also of note from [1]: apparently California is just weeks away from allowing AVs with no human operators. I'm guessing Uber wouldn't have been ready to try that out in any reasonable scale (if the state of the program is as bad as the internal docs say), though the cynical person in me thinks that, if the AZ fatality hadn't happened, they might have had a non-human-assisted AV in SF just to get some slice of the publicity.
[0] https://www.theverge.com/2016/12/22/14062926/uber-self-drivi...
[1]