I saw this in their FAQ # 57720
Installing third party cooling solutions does not void warranty on our products. Just be sure to keep the original cooling solution as it will have to be on the card if it is ever sent in for RMA. Any physical damage such as burn marks, water residue or damage, or any damage to the PCB will void ALL warranties.
This is referring to coolers...but I don't see them having an issue with replacing paste and pads if they allow 3rd party coolers. Do be careful if you do this, if you try to unscrew something and your screwdriver slips and scratches the PCB...that could be enough to say you caused damage to the card and your warranty could be voided.