No problem, reading though the info it says
1) The first device you plug in will configure the port, so always connect USB 3 capable hubs or devices first.
2) What happens if if I plug in a USB 2 device into the USB 3 port first? If you plug in a USB 2 hub first, all devices connected or "daisy-chained" to that hub will operate up to the maximum transfer rate of USB 2 speed (480 Mbps)'
So I'm guessing once its done unless you either do a PRAM reset (just a guess) or go back to a point before you plugged the device in via time machine, but I would not like to hazard a guess it may mean a complete reinstall but that seems a bit ridiculous. I would plug in USB 3 first as it may be easier all round. Here is how to reset PRAM it may be worth a try if this does happen.
http://support.apple.com/kb/HT1379