poor primus
The depth of the vortex sucking the planet in on itself looked to be all the way into its core, so would suggest it was more than just a portion being affected.
But no one complained when BW characters killed off in one season finale (like Inferno) were shown to have survived in the next, so if a future movie writer needs Cybertron around, I don't think anyone will care if they include it as if nothing happened.