Using a Sharpie permanent marker to mark a ballot will not invalidate or cancel a ballot or vote.
If the marker does bleed through to the other side, ballots are designed so that the bleed through does not touch or come near a voting area on the other side of the ballot – it will not alter or cancel any vote on the opposite side.
The Sharpie is the recommended marking instrument by voting machine manufacturers and is preferable to an ink pen because it dries quickly and will not leave residue on the ballot scanner.