Since you are already down, you could try a last ditch effort of hot plugging the card. Boot the system to your flashing environment without the card inserted, then put the card in the slot and try to flash it. Or, muck around in the BIOS and see if there is an option to not scan for card ROMs and see if that helps.
That's not a bad idea. Keep in mind, I can't even get into the BIOS. When I turn it on, it immediately shows the error message and wont let me do anything. I was going to take the card into work where I have access to some Dell OptiPlex machines, and try plugging it into one of those and see if it will let me boot and flash it back. I might try your idea tonight of yanking the card out and booting the server to the boot menu, then sticking the card in and flashing it back. What are the chances of something bad happening if I plug in the card while the system is on?