I don't know that they pretended like the last seasons didn't happen - they did mention William, and Mulder was still in hiding at the beginning. Although honesty? S8 broke me and I didn't watch S9, so I was okay with the movie not paying a lot of reference to those years. :p

But...they did end up living happily ever after! They had a fight, sure, because they needed some conflict between them during the movie, but they kiss and make up by the end. I was actually really happy with that part of it.