\documentclass{article}
\usepackage{amsmath}
\usepackage{subfiles}
\begin{document}
\section{Introduction}\label{sec:intro}
Blah.
\subfile{asubfile}
\section{Conclusion}\label{sec:conclusion}
And so, given \ref{sec:intro} and \ref{sec:middle},
therefore.
\end{document}
