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I am not sure that there is an answer to this question, but I try.

I am writing two papers; in the second I often reference to some equations reported in the first: how can I use \eqref and \label so I do not have to track all the changes in the numeration of the equations?

The papers are separated documents, I am not using \input to merge them in one file (like one does with thesis' chapters for example).

EDIT In this question, the OP sais:

I have a main document (manuscript) and a supplemental document.

But, as I said, my papers are separated files, there are no main document and supplement document.

mattiav27
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  • See the xr package, which I think will help. Not sure if this is related: http://tex.stackexchange.com/questions/123609/help-with-cross-referencing-and-altered-numbering-schemes – Steven B. Segletes Jul 26 '16 at 11:59
  • In the linked question, the OP also says 'I wonder if there is a way that I can "link" the two (make them recognize each other) so that section, equation, and figure references across documents are recognized?' That sounds exactly the same to me. – Ian Thompson Jul 26 '16 at 12:18

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