Yes the agen knows, but it is the "reporting" factor that can be the problem with MM. The transfer agent's job do not require to report who is actually shorting the company for the reason that no MM is breaking the law by shorting the company in the allotted time by SEC rules and regulations. How many of the shares shorted are naked? Who knows! The transfer agent cannot disclosed that information. Most companies set up situation to expose the shorters like in a merger situation.
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