It's beginning to look that way. Lance Henrikson recently appeared at a UK convention and gave a coy answer to a fan's question regarding a potential appearance in the X-Files sequel.
Here's an excerpt from the source:
Anyway he was asked if he would be in the next XFiles movie with the cross over storyline from Millennium and he said he wasnt allowed to talk about it at the moment but he would leave it up to us to decide what that statement meant!!
I think it means we just may be getting Frank Black. That alone in my mind(If true) makes the movie worth seeing.