Select Drives Aren't Recognized In BIOS/Windows 8.1 After Hardware Change

ThePCElitist

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May 11, 2014
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I installed Windows 8.1, Drivers, and Drives and everything was working right. Then I unplugged all of my PSU Cables and worked on my Cable Management. When I got done with that I pulled out my CMOS battery for 1 minute and then put it back in because my Windows Clock wasn't holding the right values. Then I booted into Windows 8.1 and my SSD was recognized (Primary Drive) by Windows but my HDD (Secondary Drive) wasn't. Then I plugged in my External Optical Drive and that wasn't recognized either. So I plugged in my External HDD but Windows was recognizing that. Why does Windows recognize my SSD and External HDD in Disk Management but not my Secondary HDD and External Optical Drive?
 
http://www.asus.com/Motherboards/MAXIMUS_VI_HERO/