I had this exact same problem begin on Monday 5/6, no amount of rebooting would fix it. I tried doing a full shut down but as far as I can tell that is not possible (even if I wait a couple of minutes after hitting the shut down button in the service tab, and the screen, ac, and interior lights go dark, as soon as I put my foot on the brake the car is on nearly instantaneously without any boot sequence evident).
Chatted with Tesla service, they scheduled me to bring the car in that Friday, 5/10. Thursday I was contacted by a member of the remote diagnostics team. He looked at the logs and said he "could see some issues". Friday morning, autopilot and cruise were back as if nothing had ever happened. I don't know if they did a remote reboot or if the autopilot just rebooted on its own, or some other magical fix. I asked and the technician said "No really there is no reset you can do, just the autopilot computer performed a sleep cycle and reseted." He also added that I can always try a scroll wheel reset but they didn't yet know enough about the problem to know whether that would help. He said to not bother bringing the car in for the appointment but to not cancel the reservation just in case. A few days later I got a text from him with an apology and the message that "Unfortunalety there is no fix for the issue just yet but our engineers are working on a firmware version that will bring a fix to this issue."
Autopilot kept working just fine - until this morning. The problem is back. I pulled my USB drive and rebooted - no dice. I tried a shutdown and waited a few minutes and had the same disappointing experience that left me thinking no actual shutdown of anything had occurred. Chatted with Tesla support just to let them know the problem has reoccured and gave them a message to pass along to the remote technician.
So it looks like I'll have to actually drive my own car on the freeway with my own two hands and full attention for the next week until the autopilot decides to "perform a sleep cycle and reset" or until the firmware update hits, whichever comes first. For what it's worth I'm on HW 2.5.