I am seeing this issue too, but in my case, it seems there is something wrong in bbswitch-dkms, if I remove it manually by 'sudo rm /lib/modules/4.4.0-xx-generic/updates/dkms/bbswitch.ko' I can boot into system with both intel and nvidia mode (prime-select intel or prime-select nvidia).
Since nvidia-prime depends on bbswitch-dkms, I can not remove bbswitch-dkms by 'apt remove', so the temporary solution for me is to remove the kernel module.
I am seeing this issue too, but in my case, it seems there is something wrong in bbswitch-dkms, if I remove it manually by 'sudo rm /lib/modules/ 4.4.0-xx- generic/ updates/ dkms/bbswitch. ko' I can boot into system with both intel and nvidia mode (prime-select intel or prime-select nvidia).
Since nvidia-prime depends on bbswitch-dkms, I can not remove bbswitch-dkms by 'apt remove', so the temporary solution for me is to remove the kernel module.