No it does not mean that, when you upgrade what you're doing is essentially buying the component you're upgrading from PCS - they don't take back your original component.
So if, for example (worst case), you had decided to OC your graphics card and lets say, it died. You could still upgrade it through PCS if you wanted to. You could not however legitimately claim an RMA on the graphics card because you had voided the warranty on the card by OC'ing it (I don't think the PCS graphics card suppliers allow end users to OC the cards, I know EVGA do for example for not all manufacturers allow this).