They're going to, because there is no property that will not be milked for nostalgia.
Although honestly, it could work if they played into the cynicism and uncertainty of the modern UFO phenomenon. If the "conspiracy" is a hall of mirrors comprised of psyops, lies, grift and folklore and the truth is something very weird exists but the government doesn't know what it is. Establish a "post-truth" narrative where the only thing we know is that everything we thought we knew (Roswell, Area 51, Dulce, Majestic 12) was a lie.
Maybe at some point have the in-universe version of Northrop-Grumman (or pick whatever defense contractor you like) actually make a breathrough in reverse engineering alien technology (or say it's China, to play on American xenophobia) and now the enemy isn't some vast government conspiracy but dark capitalism. Have an Elon Musk analogue, AI death cults around weird alien artifacts, SV startup culture, UFO grifters within the government, creeping fascism, all of it.
Someone could make an intelligent and interesting show that studies the nature of hyperreality, the evolution of UFO folklore as a mirror of generational fears, and the embrace of metaphysics as a trauma response to the dehumanization of modern technological society. The problem is, that wouldn't be the X-Files. Something closer to Lone Gunmen, maybe, as written by Grant Morrison, without cops being protagonists, but the vibe of the 90's and the Smoking Man and all of that is just too quaint to be plausible nowadays.
They'll do it anyway, and they'll do it badly, and they'll probably do it with AI.