Writing a thesis with Lyx / Latex

The Lyx editor is a WYSIWYM - What You See Is What You Mean editor for Latex. I have been using it for 3 years to write research articles. It is now time to compile 4 articles as thesis chapters. A collection of thesis templates has been made for Lyx. I used the default Lyx thesis template which comes pre-installed. The template makes it possible to compile many child documents into a main documents.

Modification to existing articles to integrate them as child documents in the thesis

One of my chapter title was too long to be used as page header on all even pages. This answer solved the issue: I inserted

\chaptermark{short title name} in ERT (Evil Red Text) after the chapter title.

Article 3 had an appendix which caused subsequent article 4 to have weird section number A,B,C instead of 1,2,3. I read the appendix after each chapter question and considered using  subapendix from the appendix package. But it returned an error "\AtBeginEnvironment{subappendices}" is an undefined control sequance. Maybe because I forgot to remove the \appendix option in Document/start appendix here. For the moment I decided not to use subappendices.