The surviving Atlanteans used the time machine to re-establish themselves in the past, in an era long before the arrival of the Vortex. It is not known if the Atlanteans ever used the time machine before this. However it appears to be stable technology because Ecco successfuly operates it numerous times during his quest.
In Ecco 2 the Vortex have figured out how to use the Time Machine and the Vortex Queen uses it to escape at the end of the game. Each time the machine is used it runs the risk of creating a time paradox as was shown in Ecco 2.