I don't think that the AvP movies are going to be referenced at all regarding this new EU continuity. The reason being solely this particular quote to this question: Are both AvP movies going to be canon, or just the solo movies?
"Sebela: I'm just sticking with the solo movies, because I think they build up an interesting mythology of their own that fits in well with the world we're building. I think the AvP movies have a lot of interesting things going on, but they seem to exist in their own little bubble, one that's very far away from ours, and, personally, I want to keep myself as free of all past AvP encounters, to start from a clean slate and build my own take on this mythical face-off."
To me, and I am not sure if I am reading too much into this, means that he is counting only the solo films but not so much the AvP films and plans on writing a who new expanded universe continuity. To me, that's fine because that means it's a separate thing from the old expanded universe continuity and perhaps probably not a retcon.
You said it yourself, it'll be like Batman being redone from the comics, TV and film. At least I hope you are right in that aspect.