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You might want to approach this issue on the AutoCAD side of the translation. You could have a one button operation that freezes all but those layers you want to delete. You can then select all, delete all entities, then unfreeze all layers and then purge the drawing. The purge should remove those layers you just deleted all the entities from.
That method may work out for 2 or 3 drawings but when doing 15-20 drawings at a time adds up to a lot of wasted time. You can export every other file and not include hidden items except when exporting them to Autocad dwg or DXF.