New long Chandra grating observations of the O supergiant $zeta$ Pup show not only a brightening of the x-ray emission line flux of 13 per cent in the 18 years since Chandras first observing cycle, but also clear evidence - at more than four sigma significance - of increased wind absorption signatures in its Doppler-broadened x-ray emission line profiles. We demonstrate this with non-parametric analysis of the profiles as well as Gaussian fitting and then use the line-profile model fitting to derive a mass-loss rate of $2.47 pm 0.09 times 10^{-6}$ Msun/yr, which is a 40 per cent increase over the value obtained from the cycle 1 data. The increase in the individual emission line fluxes is greater for short-wavelength lines than long-wavelength lines, as would be expected if a uniform increase in line emission is accompanied by an increase in the wavelength-dependent absorption by the cold wind in which the shock-heated plasma is embedded.