... it's probably safe to assume that The X-Files comics from both Topps Comics and WildStorm Comics, the comics The X-Files: Season 10, The X-Files: Zero Year, The X-Files X-Mas Special 2014, The X-Files: Season 11, The X-Files: Conspiracy, Millennium, and The Lone Gunmen, and the crossover comic series The X-Files/30 Days of Night, as well as the computer and video games The X-Files: Unrestricted Access, The X-Files Game, The X-Files: Resist or Serve, and The X-Files: Deep State, and The Simpsons episode "The Springfield Files" (which parodied Mulder and Scully) are set in an alternative reality. Since we never saw or heard from Special Agent Craig Willmore again after The X-Files Game, and given that Special Agents Winter and Dale from The X-Files: Deep State weren't involved in the new seasons and their cases weren't at all referenced, I'd say that it's safe to assume so. Plus, the Season 10 and Season 11 comics have totally different events and cases than the actual seasons did.