I have similar problem. I shared my game world into some sections to increase performence. In C2 i can see all of my lauouts, and by going to project folder, i see them in layouts folder (nice xml files). But where they are in html/exported mode?
I noticed, there are some references to layouts look in c2runtime.js, but still I'm not sure - is that the place where all informations about layouts are stored ? If so, what is the purpose of two xml's in my cocoon-export folder ? Is it C2 garbage, or something ?