After upgrading my Mac to OS X 10.11 El Capitan I can no longer start my Boot Camp based virtual machine because of the error:
The Boot Camp partition /dev/disk0s1 used by Hard Disk 1 is missing
The issue is caused by the major changes in OS X 10.11 El Capitan: new System Integrity Protection.
Please upgrade to Parallels Desktop 11 for Mac, which is fully compatible with the new OS X 10.11 El Capitan.
For upgrade instructions please visit KB123279.