Idea nothing. Whether an individual fan chooses to acknowledge the works of Season 8 and 9, Doggett and Reyes very much are a part of X-Files cannon. They simply can not be left out if XF3, especially if that is the final movie in the franchise. On that note, it is highly unlikly that CC and FS would leave out their chars, and even more unlikely that AG and RP would pass up the opportunity to resurrect their chars.
Just my opinion, but I think odds are looking good. =)