Re: Ewww.. SGU let's have some freaking protocol
Tens of Thousands if not millions of years could have passed between Destiny and the city ships. As the ancients looked elsewhere such as into Ascension, Destiny could simple have been forgotten about, lost or destroyed. Given the possible timescales invovled it's really not that suprising that something might have been lost/overlooked/forgotten about etc...
On the continent of wild endeavour in the mountains of solace and solitude there stood the citadel of the time lords, the oldest and most mighty race in the universe looking down on the galaxies below sworn never to interfere only to watch.