Thanks for joining the motherboard community.
I understand you have cloned your boot drive using Third Party software on another drive. Now, hard drives are not visible on Windows.
It appears to be an issue with the software you have been using to create your clone disk. Please bear in mind, your computer supports RAID levels. If you are going to create a clone for one of your drives, you can take advantage of RAID 1. This technology creates a mirror of your existing disk.
See here for more details: http://www.intel.com/support/chipsets/imsm/sb/CS-009337.htm