When using a section within a mainpage as following:

/**
 * @mainpage My Main page
 * This is my main page.
 *
 * @section mysection My Section
 * This is my section.
 */

The configuration file has GENERATE_HTMLHELP set to YES. After running doxygen (1.8.5) the resulting index.hhc file contains an error:

<LI><OBJECT type="text/sitemap"><param name="Name" value="My Main page"><param name="Local" value="index.html"><param name="ImageNumber" value="11"></OBJECT>
  <UL>
  <LI><OBJECT type="text/sitemap"><param name="Name" value="My Section"><param name="Local" value="a00003.html#mysection"><param name="ImageNumber" value="1"></OBJECT>
  </UL>

The inner <LI> references "a00003.html#mysection" which should be "index.html#mysection".
This causes an error when running hhc.exe:

HHC5013: Error: URL reference in the TOC cannot be resolved: "a00003.html#mysection".

When changing the hhc file to use "index.html#mysection" it works correctly.

This construction worked fine with older versions of doxygen (not exactly sure when it started to fail). In the cases where it worked the section of the mainpage would not be part of the hhc file at all though.