Yes and no. With power off and unplugged, non of the components will care if they are also unplugged, so rerouting cables isn't a problem. It'll only be a problem, if once you finish all the tidying up, you miss plugging something back in.
Some components, loosing connection to ground, may need to be found again (USB is good for this) but upon reboot, Windows will do this automatically and wont be a problem since all the necessary drivers are already installed in Windows, as you've not added anything new.
As long as everything is plugged back in, you'll be fine.