By the end of the original X-Files television run, Mulder is
a fugitive, having been convicted of the murder of Knowle Rohrer.
Both the "victim" and at least one member of the tribunal were "super soldiers" — nearly immortal replicants who were amassing greater and greater power, becoming the primary antagonists of the series by its end.
In the film I Want to Believe, Mulder is pardoned by the FBI and is reasonably comfortable coming out of hiding. He doesn't seem to think that it might be a trick by the super soldiers to make him drop his guard. In the new miniseries, he doesn't seem wary at all of super soldiers — they're not even a topic of conversation in the mytharc episode "My Struggle".
By the second and third episodes of the miniseries, he is comfortably situated in the FBI headquarters again — a place that was once infiltrated by several super soldiers.
Why is Mulder no longer afraid of super soldiers? What happened after 2002 to make him think that they are no longer a threat to him?