No. Not unless you change more than one piece of hardware when you put your system back together. I've never had any problem when changing just one item at a time, such as the cpu or ram. Windows should be fine. It may reboot once if you change the usb port for a usb device, for example, but that's all.
As long as ASUS sends you back the same type of MOBO (ie. same chipset, etc.) it should be fine ( though it might require reactivating of the license ) -- if for some reason they send you a new MOBO that has different components you might have to do a repair installaton to have the OS reevaluate the system devices and install the proper drivers but chances are you will get the same MOBO as a replacement so that will most likely not be needed.