SOLUTION: It turns out it was a documentclass problem. By removing prl from \documentclass[reprint,aps,prl,superscriptaddress,notitlepage]{revtex4-2} it fixed my problem.
I'm having a problem where I can refer to figures/equations/tables, etc. but not sections in my supplemental document. For the supplement, I want to add in an "S" prefix before everything, so I've redefined them at the beginning. However, this doesn't seem to be working for the sections, and I don't know why. I've created a minimal working example below.
The problem likely lies in that the sections themselves do not have numbers, however I don't see anywhere that would explicitly turn them off here for any reason.
\documentclass[reprint,aps,prl,superscriptaddress,notitlepage]{revtex4-2}
\usepackage{lipsum}
\newcommand\startsupplement{%
\setcounter{table}{0}
\renewcommand{\thetable}{S\arabic{table}}
\setcounter{figure}{0}
\renewcommand{\thefigure}{S\arabic{figure}}
\setcounter{equation}{0}
\renewcommand{\theequation}{S\arabic{equation}}
\setcounter{section}{0}
\renewcommand{\thesection}{S\arabic{section}}
}
\begin{document}
\title{\textbf{\fontfamily{phv}\selectfont
Supplemental Material: \\ My Supplement Name}}
\author{Me}
\affiliation{Department of Physics}
\maketitle
\startsupplement
\section{First Section}
\label{sec:section1}
Referring to Section~\ref{sec:section1} \\
Referring to Section~\ref{sec:section2} \\
\thesection
\begin{equation}
\label{eq:linear}
y = mx + b
\end{equation}
\begin{equation}
\label{eq:exponential}
y = y_0 + e^{ax}
\end{equation}
Referring to Eqn.~\ref{eq:linear} \\
Referring to Eqn.~\ref{eq:exponential} \\
\lipsum[1]
\section{Second Section}
\label{sec:section2}
Referring to Section~\ref{sec:section1} \\
Referring to Section~\ref{sec:section2} \\
Referring to Eqn.~\ref{eq:linear} \\
Referring to Eqn.~\ref{eq:exponential} \\
\lipsum[2]
\end{document}
