Varioref, cleveref and autonum together
Since it seems you want the \vref
command to work with Comma Separated Lists, you should use \autonum@generatePatchedReferenceCSL{vref}
as in the following.
\documentclass{article}
\usepackage[%
paperwidth=3in,
paperheight=2in,
margin=0.1in,
bottom=0.3in,
footskip=0pt]{geometry} % Only to get smaller pages for MWE
\usepackage{amsmath}
\usepackage{varioref}
\usepackage{cleveref}
\usepackage{autonum}
\makeatletter
\autonum@generatePatchedReferenceCSL{vref}
\makeatother
\begin{document}
\begin{align} x \label{eqnx} \end{align} % referenced, must have number (1)
\begin{align} y \label{eqny} \end{align} % referenced, must have number (2)
\begin{align} z \label{eqnz} \end{align} % not referenced, must not have any number
\pagebreak
\vref{eqnx,eqny}
\end{document}
From section 3.3 "Reference commands" in the documentation:
For reference commands expecting a comma separated list of label names as an argument, you can use
\autonum@generatePatchedReferenceCSL{NewReferenceCommand}
.