Nah, it's rebooted, not destroyed. Also, they mention that they have Fun Shaundi saved as a backup on a computer on the ship.
Oh, right. There is that.
Personally the time travel scenario I'd like to see is the Saints heading back in time to the plane, and charging and beating the shit out of Zinyak when he arrives to get Gat.
You know this interference could somehow affect Loren and turn him into the supervillain SR3 was building him up as before he got squished.
Just saying there's a lot of in-joke potential there..