You can still synchronize them, it's just that "synchronize" takes on a more complicated meaning. Both sides can use their clock, and the known positions of the two clocks over time, to predict the time that the other clock should be reading. The time deltas are no longer the same on both sides, but you can still transform between the two in order to compare them and detect errors occurring.

More pragmatically, we'll probably agree on a standard centralized time (i.e. International Atomic Time) and everyone will translate between their own locally perturbed time and the standardized time when synchronizing.