Just thinking aloud, but, say you copied the contents of each file into a single drawing, could you not create two selection sets of each set of entities, and, compare the DXF data for each entity in SelSet 1, with that of entities in SelSet 2, and if a match is found, remove both entities from the SelSets?
Of course, this is a completely "brute-force-sledge-hammer" approach... but then, if handles do not live up to their expectations, then this may be another option.
EDIT: this wouldn't work as all the locations would be different... stupid idea. New Idea! Ok, how about finding a base point and copying all the entities into one drawing, and sitting both copies on top of one another. Then use OVERKILL to remove duplicates, leaving you with the uniques