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There is a way to make a selection set using mapfilter. If you could populate a list, then use a lisp routine to do each iteration, that is one path. The list can be created by converting a screenshot of the project browser. I use SnagIt that has not only the screen capture, but does it while scrolling and converts to text.
I'm not familiar with Doxel's expected file format or data, but maybe you can isolate each Revit assembly, manually or by creating assembly views, then export the view to DWG. The assembly view's name will likely reflect the assembly name, but you can also change it as you export. The resulting DWG has each part as a named block and the DWG will be your named assembly block. Import/Insert all the assembly blocks into an empty DWG to combine, if needed.
Doxel is requiring each assembly to be saved as a block in one combined DWG. Sounds like your method would work but i would also have hundreds of assemblies per floor. I was hoping to be able to save each assembly as 1 block all at once. And not have hundreds of cad files to create and import per floor. I know scripting could potentially do this, but i dont have the knowledge to create this lisp