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With the current code the document gives the same reference twice.

\PassOptionsToPackage{square,numbers,comma,sort&compress,super}{natbib} 
\documentclass[aps,prl, twocolumn, a4paper,superscriptaddress]{revtex4-2}
\usepackage{multibib}

\begin{document}

\bibliographystyle{plainnat}
\bibliography{mybib1}

\bibliographystylerec{plainnat}
\bibliography{mybib2}

\end{document}
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