Imagine an X-Files movie without David Duchovny and Gillian Anderson. Or, even one that didn't feature them prominently. Obviously, this is not the case with XF2; it's probable that they will indeed be re-introduced early on in the movie and will appear a lot throughout the first act in their own part of the grand scheme of the plot -- the synopsis shared with Moviehole is likely just the subplot that doesn't involve them, perhaps because it's being shot first and/or separately. Anyway, as always, the truth is out there, somewhere, and it's only a matter of time before we hear what the real deal is. Moviehole additionally reports that casting is currently happening in Canada, so hopefully we'll hear some news on that soon, as well. As we previously learned, the movie is supposed to begin shooting in December and is set to hit theaters next July.
*UPDATE: Apparently the plot/character details are incorrect and director Chris Carter is merely using old character descriptions in order to more-secretly cast for XF2. Thanks to all the commenters for pointing out the correction.