Maybe I need to pay more attention to the forums (haven't been there in a while), but how could the Xenon be attacking again? The Kha'ak I can understand—they've got gateless jumpdrives—but the entire point of shutting down the gates was to stop the Xenon from going anywhere. Did they just accelerate to relativistic speeds and hoof it to Commonwealth space or something?
Apparently, one of the first things you're able to do in the "main" storyline is reactivate the Portal Network. The Xenon have most likely spent the last millennium both replacing the forces they lost in Terran Conflict and Albion Prelude, as well as strengthening their remaining forces, so once the Portal Network is back online, of course the resident Omnicidal Maniacs are gonna take advantage of it.
Several extra points. The events in X: Beyond the Frontier were triggered by a special Xenon ship with a gateless jumpdrive being captured by the Terrans back on Earth, so there's really nothing stopping the Xenon from continuing to develop that. Secondly, if the unfocused jumpdrive sectors are saying anything, it's that the Xenon have expanded into deep space sectors without functional gates for them to pass through or to lock their jumpdrives onto. In either case, shutting down the entire gate network did more harm to the X-Universe races than it did to the Xenon, a case of Nice Job Breakingit Hero for the Ancients.