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.
xrpackage, 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