Big problem with medias url and folder

Hello,
I would be really really happy to have an anwser, even if it’s impossible 🙂

I had a developper who export an old php blog (it wasn’t a cms) and build a new wordpress really great. He left me during the process : I have to export this blog into 2 MU sites. I already did that, it’s not a problem. But! Big but !
He didn’t worked with the good practice on librairy. He worked with ID (that what he said).
So I have my posts with good thumbnail, even if he put aaaaall images (8000) in a same folder (/upload without under folder with dates).
When I want to export a part of this blog in xml I think wp can’t find images so nothing in xml code on url images, and impossible to import…

Do you see my problem and is it possible to make something…?
The posts have a featured image, but I don’t know where it’s declared, because xml export everything but images.

I have to find a way to tell wp to export real image it has in thumbnail/featured image (and not the way it used to, in folder/yyyy/mm/dd) OR something to rebuilt the librairy and put images in good folders…

Thank you a lot for your answer.
I can pay a bit the one who can help me if it’s complicated, but I have 1000 posts to repost in 2 differents domains, and it could be really long to reimport featured images with my hands :/