You can also tell calibre whether to put it at the start or the end of the book via an option in the MOBI Output settings. You can turn this off by an option in the MOBI Output settings. When converting to MOBI, calibre detects the metadata ToC in the input document and generates an end-of-file ToC in the output MOBI file.

This is because the HTML to ZIP plugin automatically converts the HTML files to a standard encoding (UTF-8). Note that when converting HTML files, leave the input encoding setting mentioned above blank. A common encoding for many files from the web is cp1252 and I would suggest you try that first. HTML files from different sources often have different encodings, so you may have to change this setting repeatedly. Now when you add HTML files to calibre they will be correctly processed. To do this go to Preferences → Advanced → Plugins → File type and customize the HTML to ZIP plugin, telling it what encoding your HTML files are in. When adding HTML files to calibre, you may need to tell calibre what encoding the files are in. The command-line tools have an ebook-convert-txt-input -input-encoding option. This can be done in the GUI via the Input character encoding field in the Look & feel → Text section of the conversion dialog. Knowing the encoding of the source file: calibre tries to guess what character encoding your source files use, but often, this is impossible, so you need to tell it what encoding to use.

Calibre 6.22.0 free