Ok, well it's a bit confusing and complicated.
Basically, we have been asked to upload documents that we have already uploaded, namely valid passports and and proof of status for my daughter. (visa) This led to a horrible discovery that her visa is actually expired. BUT when we landed here a year and 1/2 ago, the border agent said the visa was attached to her passport, and as long as we renewed her passport she would be legal. We also crossed to the states and back many times with the visa expired, and they explained again that the paper is attached to the passport and if the passport if updated the visa is as well.
But I'm assuming for PR that must be the problem and we should have gotten it renewed? Is there any super fast way to do that? Can we drive to the border and do it there?
And this does not answer the question of why they asked for my son's passport again, even though we provided both a French and American passport. Both are valid, although the US one expires in June.
