It will be a replacement motherboard. It's not the same motherboard repaired, but it's still the exact model but a brand new one. If you understand what I mean.
It's best to clean up and apply new thermal paste.
Also if you call Microsoft and explain to them that you replaced a dead PC they may activate it for you.
EDIT: if your new CPU come with a heatsink/fan it'll have the paste on it. Just clean up the CPU.