Thanks, that's useful to know. Could you have a close look under a magnifying glass and tell me if the capacitors next to the crystal are also missing? I'd probably be able to solder the crystal back on if I needed it, but the capacitors would be impossible.
The only situation where this would be important is if someone needs real-time accuracy in low-power mode (otherwise the RTC can be emulated in software). It would be interesting to see how much power the Due takes with the SAM3X in a very low-power state.