Providing the server's bios can see it, I don't think there would be an issue as far as the actual flashing it is concerned. However, there is one possible fly in that otherwise goodly ointment, and that would be if it is no longer recognised or the server claims it to be a "foreign object" after flashing it. If you have to reboot during the flashing process, you might lose access to the card, if you see what I mean. The card won't be damaged in any way though and can still be recovered again in another mainboard if it comes to that. I would say, give it a try and let us know how it goes
Odd issue on the thumb drive, try another one, or use an EFI shell and flash the card that way. I find that the cheaper the thumb drive, the better DELL supports it!