I wanted to upgrade the software in my SSD but it would only work if the SATA drives were set to use AHCI (Advanced Host Controller Interface) in the motherboard BIOS (it was set as IDE). So I edited the Win7 registry to use AHCI and changed the BIOS to AHCI, on rebooting I was able to flash the SSD no problem.
A side effect of using AHCI is that all SATA drives become plug and play,
including your boot drive and other internal drives. They are added to the 'Safely remove Hardware and Eject media' tray icon.
Being curious I tried to eject my Data HD (a separate 1Tb Seagate hard drive, not a partition on my boot drive which is a 50Gb SSD), it was removed from the list but was still accessible.
On reboot later I got:
Bootmgr missing
Ctrl+Alt+Del
I tried using the Win7 install DVD to recover the missing file but that didn't work, luckily I'd made a full backup image of the whole SSD drive before I flashed its BIOS so I was able to boot the Paragon recover CD and replace the MBR & OS etc.
The motherboard BIOS is back to IDE.