I had my Macbook running in Boot Camp. I used the Boot Camp Assistant and selected to reboot into OS X. When it rebooted, it immediately started up into Recovery mode. I did a verify disk and it said that the EFI partition had a problem, so I clicked repair disk and restarted.
On the next restart, there were no startup disks available. "Internet Recovery" is my only option. When I boot into recovery, I see both partitions there, I can mount them and the data is intact. Also, the Startup Disk tool shows both the Boot Camp and OS X paritions as available startup disks, when I select one and hit reboot, it still just shows the flashing folder with a question mark icon.