First off, and in all sincerity, make sure the banner you buy is meant for double sided printing.
Second, depending on how your image is laid out, you may need to rotate the image to get printed again.
I don't know what kind of machine you are running, but I have a Mimaki, so here's what I do: all rolls aren't perfectly symmetrical, so the easiest way to register is to advance out just a bit, mark the side and bottom with tape. Go ahead and run it, release the pinch rollers, roll it back up, flip the roll, advance out again to meet with the registration, print again.