I personally would not want to see an official conclusion to the FreeSpace narrative. It would immediately invalidate all the SCP team's hard work and the storylines of every single post-capella mod.It's been discussed to death, and the short answer is, "only if you let it."
Yeah, I guess if you're willing to ignore canon it wouldn't affect them. It would kill immersion for me, but that's just the way I perceive things.
Let's just save us all a lot of trouble, and say that this can only happen if any individual decides it's so for them. It is not automatic. None of the post FS1 campaigns were invalidated by FS2, same would be for a hypothetical FS3. It might make it awkward, but wouldn't "invalidate" any mods or campaigns. This has been suggested many times before on this subject.
At this point, any mod with a storyline that doesn't contradict the established narrative can claim a small amount of canon plausibility, even if it will never become a canonical reality. FS3 would eliminate that and throw every post-capella campaign into alternate-universe territory, thereby invalidating their storylines in a canon sense.
And let's not forget that if FS3 was moddable enough (and it might well be) it would either (A) compete with the SCP and split FreeSpace mods between two different programs, making it significantly harder and costlier to play all of them, or (B) eliminate the SCP all together.
I stand by my original statement that FSO is a perfectly good, non storyline-crushing substitute for FS3.