Xtreme 2, of course. stupid me. I completely forgot about Xtreme 1's plot.
Now that you mention it, given that Reploids are built for specific purposes and therefore made 100% for it, i doubt they would actually need such a program. That would defeat the purpose of using robots in the first place. Iris not being sure what to do with herself is more likely, given her unique place in the Repliforce.
As for X5 and the Repliforce, It's hard to say what survived X4's Repliforce into the future. But obviously, despite X5 implying it has been a while since X4, the events are still fresh in the minds of people like Skivver/Pegacion. though that could be due simply to dramatic reasons. (he needs to babble about SOMETHING as a Maverick) So it was obviously a blow, and it's likely Repliforce's ground army was disbanded, leaving whatever other sections on their own. and even if they wanted to do something, with The virus everywhere and mayhem ruling supreme, it's not like they could do much. The virus was even affecting regular non-sentient machinery. The Repli air force probably couldn't do much. And then there was the matter of the bombs placed all around their airport. And then, a bunch of the force probably went Maverick as well, causing internal chaos, much like with the Hunters, who by the end of the whole ordeal, were so badly battered, they had to disband all units into a single core.