They don't measure the missing ice either. They estimate it based on all kinds of things (mostly models based on what they guess the answer should be). Some of the actual measurements include the deviation in satellite orbit as it passes over Greenland, from which they estimate the change in gravity, which leads directly to an estimate of the change in mass. Since the rock is unlikely to be changing on the time scale of a year or so, they assume it's a change in ice mass. Given a typical annual precipitation of zero in central Greenland, it's a safe bet that any change is mass is due to ice melt.
And how is sea level defined - the average over the year? So more ice has melted than usually? Even then, it seems normal that not the same amount of ice would melt every year?