These mean the same thing. However, "It does work" would more often be used as an answer to a question or to correct a previous statement someone made. The speaker is probably adding that additional word "does" to clarify something.
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In my opinion, add auxiliary verb to emphasize more about what you mean in your sentence.
ex : I really hope that you are happy
I really do hope that you are happy ( from 500 days of Summer )
September 11, 2017
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