Replacing the motherboard and CPU shouldn't have any effect on the programming installed on the HDD/SSD other than Windows (maybe Office if you have it because MS can be a bit sensitive). You will probably have to reactivate Windows, but even that's pretty easy, and is automatic if it's registered with a Microsoft account. (After doing the hardware upgrades, you might have to reboot and log in to your Microsoft account for the automatic actiivation to occur. If it doesn't activate, go to Settings>System>About>Product Key and Activation, select to activate by telephone, then switch to activation by text messaging when offered, and it's a pretty simple process.) If you do have Office, and have to reactivate it, you can do so from inside any of the Office applications by going to File>Account. It's then the same process as reactivating Windows. Of course, if you wipe the drive and start everything from scratch, all licensed software will have to be reactivated. I recently did these hardware upgrades on my desktop, had to reactivate both Windows and Office, but StartIsBack stayed registered. (I bought a new StartAllBack licenses for lmy desktop, laptop, and tablet anyway because it's so cheap.) Hopes this helps you.
Edited to add: If you need to reactivate Office, MS wll ask how many computers you have it installed on. Just say one and it should reactivate.