So some time ago, my computer's manufacturer (Samsung) sent me a disc because I requested one; basically, my laptop's serial number had worn away and the system restore partition had gone bad. Basically, customer support told me, "We'll send you a disc that Windows won't ask for your serial number" (in essence, it by-passes the activation procedures but still registers it as a legit copy of Windows which can be updated and upgraded and such). http://i.imgur.com/T9kEb.jpg

Will using Win Toolkit with an .iso of the manufacturer's OEM disc affect the way this works? I.E. Will it eradicate whatever code it is that allows me to bypass the Windows activation procedure?

No, it should not hurt it

I don't tend to touch anything to do with activation. So no, it won't affect it.