How to convince a journal editor that my paper is not a duplicate? Recently, I submitted two manuscripts in two different journals. The papers are related, but their contents and purposes are different; and they also made use of different data sets.  One of these manuscripts got accepted for publication, but one of the reviewers for the second manuscript informed the editor the paper was a duplicated paper that he or she recently reviewed.  Evidently, that the same reviewer has reviewed my both manuscripts. However, the editor has asked me to clarify and provide evidence that my paper is not a duplicate. So how should I respond to convince the editor and reviewer that this paper is a legitimately separate work?
Just enumerate in which ways the two papers actually differ. As you already do in your question above: they differ in (i) contents, (ii) purposes, (iii) data sets. 

The reviewer may of course still think that these differences are not large enough to warrant a second paper. In that case, you need to reconsider whether you actually think that the second paper can stand alone. But your first step is articulating how you think the two papers are different.