Why did Hyperion stop bombing Sanctuary?
In the mission Bright Lights, Flying City, after losing its shields and getting bombed by Hyperion, Sanctuary, as foreshadowed by the mission name becomes a flying city.
Why did Hyperion then suddenly stop bombing Sanctuary?
Lilith contacts Hyperion on an open ECHO channel after you reach Sanctuary again, inviting them to go ahead and try. But she reminds them that every projectile they fire costs Hyperion billions of credits, and she can always teleport the city again. (She later admits to Roland that she probably can't - it took a lot out of her, and she might just as likely 'port the city into a mountain - but of course she'd never tell Hyperion that.)
I'm guessing you will end up missing this conversation if you turn in "Bright Lights, Flying City" to Roland without stopping to listen.