From MS community website.
Q. If my customer asks me to upgrade a PC with new hardware components, when is a new operating system needed? When would the PC be considered "new"?
A. Generally, an end user can upgrade or replace all of the hardware components on a computer—except the motherboard—and still retain the licence for the original Microsoft OEM operating system software. If the motherboard is upgraded or replaced for reasons other than a defect, then a new computer has been created. Microsoft OEM operating system software cannot be transferred to the new computer, and the licence of new operating system software is required.
If the motherboard is replaced because it is defective, you do not need to acquire a new operating system license for the PC as long as the replacement motherboard is the same make/model or the same manufacturer's replacement/equivalent, as defined by the manufacturer's warranty.
So according to this if you replace the defective MOBO with the same mobo then it would be legal. Since you bought a new computer you might have to plead a little when you call MS.