I can attest to the fact that there's no difference between a fic being finished and it not being finished. If a new development comes up in a fic in progress that comes across as incredibly stupid, it can certainly affect the length of the mission, but otherwise there's no difference.

I've had four missions total where I began them while the fic was still in progress, and nothing really changed all that much.

Sometimes I take on a fic-in-progress if that fic has already done something to totally break the canon. What I do then is take a 'snapshot' of sorts when I start a mission. If I begin a mission and chapters 1-4 are posted, I spork only chapters 1-4 regardless of what other chapters or edits are posted in the meantime.

This is because I usually have an idea of where the mission is going, and if I tack on more and more content, it ruins the run of the plot. Like any story, once I reach the climax, there's going to be falling action. I don't want to have to pick up, say 'just kidding, there is more' and keep going.

...that there pretty much is no difference. Granted, I'm not official, but I've read a lot of PPC fics and it doesn't seem to matter either way; the PPC still interrupts it after gathering enough charges and kills the Sue. After that, even if the fic continues, the Suefluence is gone (unless there's a sequel to it, in which case the Sue must be executed a second time).
So there's my thoughts on the subject.
Oh, and I don't know about anywhere else, but I think you used the semicolon just right in this post. If in doubt, however, I'd just separate it into different sentences...or Google semicolon usage. Whatever floats your boat.