Victor Ivrii reported on TeXhax issue with xr-hyper package. I've found that the tex4ht configuration is identical with xr package. There are two issues: \externalcommand has additional optional argument in xr-hyper, it ends in the document, causing compilation error, because it is before \begin{document}. The other issue is that \newlabels defined by hyperref the aux file have 5 arguments instead of two, but tex4ht macros read only these two, so the rest of them is executed at wrong place.

I think I've fixed these issues and commited the fixes to the repo.

Sample files:

%%%%%%%% sample.tex
\documentclass[12pt]{memoir}
\usepackage{xr-hyper}
\usepackage{hyperref}
\usepackage{bookmark}
\usepackage{nameref}
\externaldocument[Alpha-]{Alpha}[**some url**]
\begin{document}
\ref{Alpha-three}....\nameref{Alpha-three}
\end{document}
%%%%%%%

%%%%%% Alpha.tex
\documentclass{article}

\usepackage{xr-hyper}
\usepackage{hyperref}
% \usepackage[capitalise,noabbrev]{cleveref}
\usepackage{nameref}
% \crefname{equation}{}{}

\begin{document}

\section{MyTitle}\label{three}

\end{document}

%%%%%%