I've seen interesting methods for exporting prebuilt scenes into external programs for texture baking... people use scripts in each prim to have it export its properties in a pm, then copy/paste into a file that you load via script in your modeler. It'd take some time to get it into a single surface mesh, but completely doable.
Good luck on over 6k prims though. I suppose you could use one in a parent of each linked set but still tons of work.
edit: unless you're talking about fully exported data, which I haven't worked with and may be against the SL eula?