When you install the new OS, I'm assuming it will be Linux, it will set up the boot sector for you. So, in other words, you can start fresh if you want to and let the installer do everything for you.
EDIT: the "bootable bit" is the MBR (Master Boot Record) it cannot be moved and is always at the beginning of the disc.
BTW, always back up anything you must not lose such as important personal files.
Last edited by k3lt01; 02-12-2012 at 08:02 PM.