Ok all resolved now. It turns out my PC was set up in a RAID config, but somehow the BIOS settings had reset and the SATA config had reverted to IDE, not RAID - no idea how though...
Anyway, amending this back to RAID and restarting means Windows boots as normal.
Many thanks for all the help and advice. Turned out to be a two second fix. Apparently this is the most common cause for the "Missing Operating System" message, so anyone else, look here first!