Symptoms

Your project contains an HTML build which is followed by a CHM build and while the CHM build is fine, the HTML one is missing files such as topics, library items...


Solutions

This is due to the fact that most of the temporary files generated by the CHM build overwrite existing files generated by the HTML build. And by default, the CHM build will delete those temporary files after successful generation: the HTML build is therefore missing some files.

The best solution is to generate each build into its own specific folder to avoid such unwanted interactions.