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I was logged in with a temp profile, and nothing would run except for Regedit and Command Prompt. My system drive was also being mounted as D: rather than C: After doing a bunch of research I found the issue was related to a registry key at HKLM\SYSTEM\MountedDevices and I just needed to rename the key \DosDevices\D: to \DosDevices\C: (and vice versa). After a reboot everything was working perfectly again.
There was one other oddity though. In Disk Management the PCIe SSD (which now contains a single volume D:) is listed as Disk0 meanwhile the disk containing my system volume C: is listed as Disk1. I was under the impression that while strange this was nothing to be concerned about.
So the issue started when I brought the PC to the end user, he has an external USB drive. I mounted this drive as B: for him (his preference), and everything was fine, but when I rebooted the PC it no longer boots to windows.
I would reach the Windows Boot Manager and get the “Windows failed to boot” message. I had the option to launch startup repair but it would start loading windows files and suddenly bring me back to the Failed to boot screen, starting Windows Normally also would fail. I tried putting in a Windows Install Disk to reach startup repair from there but I recieved a message: “This version of System Recovery Options is not compatible with the version of Windows” (I think this issue is because the install disk does not have the Intel RAID driver loaded). When I unplugged the External Hard Drive, I was able to get to the startup repair, I was met with a message that no OS was found and it asked me to load storage drivers. I loaded the drivers and it immediately asked to reboot itself. On reboot I could again boot to Windows, but that just put me at square one, and when I tried reconnecting the external HDD the same issue occurred.
Thinking the issue was related to the BCD I tried following the steps here http://pcsupport.about.com/od/fixtheproblem/ht/rebuild-bcd-store-windows.htm but it didn’t resolve the issue. I’m also now receiving an new error when I try to boot with the external HDD attached error code 0xc225 and don’t have the option to launch start-up repair. Removing the external HDD then selecting “use last good configuration data” will again allow me to boot.
Any help would be really appreciated I’d like to avoid reinstalling Windows and starting over considering the rest of the PC is good to go.
I ended up reinstalling Windows and starting from scratch anyways because I was concerned that Windows was seeing the C:/ volume on Disk1 rather than Disk0, and the network driver became very strangely uninstalled. Assumed these were surface issues to potential larger problems down the road, and figured I would cut my losses.