[...] The current NTP technology has no provisions for mobile servers and clients, where range and range rates can vary with time, and only minimal provisions for intermittent connectivity. In the Mars internet, orbiters and surface stations may have only intermittent connectivity, while in the DSN segment real-time connectivity is possible only at scheduled opportunities and then only with very long delays. These considerations are mitigated by the fact that ranges and range rates can be predicted with some accuracy from the known positions of the spacecraft bus, orbiters and surface stations using ephemerides maintained by astronomical means.
[...] It may will happen that residual clock frequency offsets may introduce considerable error if the time between updates is relatively long, as would be expected during communication opportunities between Earth and mission spacecraft. After a few measurements the frequency can be disciplined in the usual way, but this affects the position and velocity vectors and residuals with respect to the ephemeris. What makes frequency-induced errors more nasty is that the frequency may fluctuate due to spacecraft thermal cycles and power management.
I think they're not taking relativistic effects into account, but I'm not totally sure...
Current Music: S.U.N. Project -- Sexdrugs + Acidtrance ♬