Problem with Appendix sub-indices

Question

Is it possible to index the sub sections of an Appendix, both in the table of contents and the Appendix itself? At the moment, what I am getting is something like the picture attached; The subsections are indexed in both locations, yet the the capital letter (e.g. A) is missing and the numbering starts with a dot (.). Any ideas?

EDIT1: The same issue appears in the "List of Figures" and "List of Tables" as well. In that case, apart from capital A, dot is also omitted.

EDIT2: Here is the project.

Answer 1

I had a closer look at your project file. In my opinion your document class isn't a good choise.

Nevertheless your document class based on the standard document class book.

If you use the command \backmatter the internal conditional \if@mainmatter is set to false. This means that that \chapter doesn't get any number nor prefix.

To show this behavior here a little example:

\documentclass{book}

\begin{document}
\chapter{foo}
\backmatter
\chapter{bar}
\end{document}

Based on this information the level section with the prefix number \thechapter can be printed because you are using \backmatter.

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At this point I want to recommend one of the modern document class memoir or scrbook. Both are well documented. I also recommend that you should avoid such templates. You will never know what the document class do.