I've also fixed it for the Xr package. I think we can fix this now.

reference and screen shots at

https://tex.stackexchange.com/questions/641726/problem-using-tex4ht-with-xr-hyper-when-other-documents-are-in-separate-folders

I am splitting my large document into smaller separate documents, where now each chapter will be compiled separately, as separate PDF file (not using \include or input, but as a separate document with its own title and \begin{document})

But I still need to have reference from a main document to the other documents to build tables and references.

So I am using xr-hyper. Which worked well. I have this MWE tree to show my current set

main.tex
|
+------ chapter_1/ch1.tex
+------ chapter_2/ch2.tex

I put each chapter in separate folder to reduce clutter. This is what my main.tex, ch1.tex and ch2.tex look like

%main.tex
\documentclass{book}
\usepackage{xr-hyper}
\usepackage{hyperref}
\externaldocument{chapter_1/ch1} %notice folder name included
\externaldocument{chapter_2/ch2}
\begin{document}
See problem \hyperref[1]{1} below and problem \hyperref[2]{2}.
\end{document}

and ch1.tex which is inside folder chapter_1/

\documentclass{book}
\usepackage{xr-hyper}
\usepackage{hyperref}

\begin{document}
\chapter{chapter 1 in document ch1.tex}
\section{some section name}
\subsection{problem 1 from some book}
\label{1}
This is problem 1
\end{document}

and ch2.tex

\documentclass{book}
\usepackage{xr-hyper}
\usepackage{hyperref}
\begin{document}

\chapter{chapter 2 in document ch2.tex}
\section{some section name}
\subsection{problem 2 from some book}
\label{2}
This is problem 2
\end{document}

Next, compiled ch1.tex,ch2.tex and finally main.tex in this order using lualatex. Now I opened main.pdf and the links there correct and work.

Next, I did the same for tex4ht. Compiled ch1.tex,ch2.tex then main.tex in this order, all using the commands

make4ht ch1.tex 'mathjax,htm'
make4ht ch2.tex 'mathjax,htm'
make4ht main.tex 'mathjax,htm'

Then opened main.htm and it shows correct output

Now here is the problem, when I click on the link, it drops the folder name from the link. The link for 1 says

ch1.htm#x1-30001.1.1

instead of

chapter_1/ch1.htm#x1-30001.1.1

So the link did not work.

By manually editing the link and adding the folder name chapter_1/ to it, then it works and opens chapter 1 page correctly.

I can fix all of this by having all separate documents (main.tex, ch1.tex and ch2.tex) in same top level folder.

But to reduce clutter, and since I have many chapters that I want to make now completely separate PDF files for each chapter (but still have cross references from main document to them), it will be much better to have each in separate folder to make it easier to manage and reduce clutter in same folder, since I need to compile each one separately now.

This looks like a bug in tex4ht, in that it drops the folder name from the reference. Or Am I doing something wrong?

TL 2021