The weapon existed outside of time (but could return to real space whenever it felt like it.) which is why they didn't change when the universe was changed, because they were outside the universe.
No one on the weapon got older since they were outside time.
(Bad fake science)
It's possible that some of the crew on the weapon who were too close to the core when it detonated were erased along with the raw materials of the weapon so that the new timeline wasn't completely like the virgin timeline before Annorax started played silly buggers.