So a few weeks ago I decided to re-purpose a server which was previously utilized as a freenas head unit running some lower tier SATA disks for nfs vm storage. This device was set to boot to freenas off a usb key.
During the Windows 2008 R2 installation process, I kept getting the error "Boot Logical Drive is Configured but is missing or offline" error. To troubleshoot, I've updated firmware to the latest, reset all array config settings & rbsu information via the HP Smart Start boot disk to no avail.
In the end, it turns out that I needed to F8 during the array setup screen to get to the ROM controller's config menu. Select Boot Volume > Direct Attached Storage. Escape out and save changes.
I have no idea how this got messed up in the first place, perhaps it was when we first set freenas to boot off usb.