I don't deal with assemblies that large, but this might help (as long as you have AAX and are using top-down design). Make sure the top-level assembly is the active model in the drawing, and regenerate that. In instances where I want to be absolutely sure, I would close the drawing, erase not displayed, open the top level assembly, regen. that, then open the drawing. When you open the drawing you should see in the dashboard that each instance and flat pattern is being regenerated. This is the only way I know of getting it to work, and thus far it has not failed me.