It was a USB3 drive in a USB2 slot, which I've read is not the best way to go about this, so I've ordered some USB2 drives which should arrive shortly, and that will be my future flash drive. With a spare on a shelf, ready to go if the main drive goes to flash-heaven.
I will try to put the drive into a USB2 slot directly into the motherboard, it was in a front-chassis connector, so that will be my final attempt of redemption. Otherwise I've pretty much come to terms with the fact, that I need to reconstuct my server.
I was, however, smart enough to label all of my drives, so I know which ones are parity 1 and 2, and disk 1-10 with 2 cache-drives.
It would be freaking awesome, if I could get the config-folder off the faulty flash-drive though.