I have a tex file
\documentclass[reqno]{amsart}\usepackage{mathtools,hyperref}\mathtoolsset{showonlyrefs}\hypersetup{ colorlinks=true, linkcolor=blue,}\usepackage[overload]{empheq}\begin{document}\section{Intro}\begin{subequations} \label{eq1} \begin{empheq}[left={\eqref{eq1}\quad\empheqlbrace}]{align} A & = B , \label{eq1:a} \\ C & = D . \label{eq1:b} \end{empheq}\end{subequations}System \eqref{eq1} contains the subequations \eqref{eq1:a} and \eqref{eq1:b}.\end{document}
I set \mathtoolsset{showonlyrefs} to suppress numberings of un-referenced equations. The numbering of \eqref{eq1} does not show up. On the other hand, if I remove \mathtoolsset{showonlyrefs}, then everything is fine:
Could you elaborate on this issue and how to fix it?