Here's the quote from X-Files News:
"I ran into Annabeth Gish at The Business of Being Born premiere in Los Angeles last night. She confirmed that neither her or Robert Patrick would be appearing in the second X-Files movie. She did say that Chris told her that if the second movie does well, she'll be in the next one."
The X-Files 2 is currently being filmed in Vancouver and gearing up for its scheduled summertime release.