Classe yathesis : « emergency stop » disparaissant après une dizaine de compilations

\documentclass[mainlanguage=english,secnumdepth=subsubsection,space=onehalf,12pt]{yathesis}%secnumdepth=subsubsection
%version=inprogress|inprogress*|submitted|submitted*|final|draft
% Chargement manuel de packages (pas déjà chargés par la classe yathesis)
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{kpfonts}
\usepackage{minitoc}
\usepackage{booktabs}
\usepackage{siunitx}
\usepackage{pgfplots}
%\usepackage{floatrow}
\usepackage{caption}
\usepackage{microtype}
\usepackage{varioref}
%\usepackage[xindy,quiet]{imakeidx}
\usepackage[autostyle]{csquotes}
\usepackage[backend=biber,
sorting=none,
backrefstyle=two,
url=false,
doi=true,
safeinputenc,
style=numeric-comp]{biblatex}%biblatex style chem-angew superscript
\usepackage{hyperref}
\usepackage{pdflscape}
%\usepackage[demo]{graphicx}% delete the demo option in your actual code
\usepackage{enumitem}
\usepackage{booktabs}
\usepackage{bm} % \bm{}
%\usepackage[super,square]{natbib}
\usepackage{longtable}
\usepackage{pdflscape}
\usepackage{multicol}
\usepackage{amssymb} % \triangleq
\usepackage{amsfonts} %\matbb, 
\usepackage{algorithm}
\usepackage{mathtools}
\usepackage{algorithmic}
%\usepackage[table,xcdraw]{xcolor}
\usepackage{graphicx,subcaption}
%\usepackage{amsmath,amsfonts,amssymb,amsthm}
\usepackage{chngcntr}
\usepackage{multirow}
\newtheorem{defn}{Definition}[section]
\newenvironment{remarque}{\textbf{Remark:}}{}
\newtheorem{assum}{Assumption}[section]
\setcounter{secnumdepth}{3}
\pgfplotsset{compat=1.12}
\usepackage{hyperref}
\usepackage{footmisc}
%\usepackage[xindy,acronyms,symbols]{glossaries}
%
% (Facultatif) Génération de l'index (obligatoire si un package d'index, par
% exemple « imakeidx », est chargé):
% \makeindex
%
% (Facultatif) Spécification de la ou des ressources bibliographiques
% (obligatoire si le package « biblatex » est chargé) :
\addbibresource{Paper01Const.bib}
\addbibresource{Paper02.bib}
\addbibresource{Paper03.bib}
\addbibresource{Paper04.bib}
\addbibresource{paperSOA.bib}
\addbibresource{QianYangPapers.bib}
\addbibresource{PaperKane.bib}
\addbibresource{FuzzyLogic.bib}
%PaperKane
\bibliography{Paper01Const.bib}
\bibliography{Paper02.bib}
\bibliography{Paper03.bib}
\bibliography{Paper04.bib}
\bibliography{paperSOA.bib}
\bibliography{QianYangPapers.bib}
\bibliography{PaperKane.bib}
\bibliography{FuzzyLogic.bib}
%
% (Facultatif) Génération du glossaire (obligatoire si le package « glossaries »
% est chargé) :
% \makeglossaries
%
% (Facultatif) Spécification de la ou des ressources terminologiques :
% \loadglsentries{}
% \loadglsentries{}
% \loadglsentries{}
%
% (Facultatif) Configuration des styles du glossaire et de la liste
% d'acronymes :
% \setglossarystyle{}
% \setacronymstyle{}
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Début du document
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{document}
%   
%\include{chrAbstract}
%
% (Facultatif) Chapitre de remerciements :
\include{prepares}
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Début de la partie principale (du « corps ») de la thèse
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
\mainmatter
%
% Chapitre d'introduction (générale)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% chapter 0: introduction 
\include{chapter0}
%
% chapter 1: 
\include{chapter1}

% chapter 2: SYSTEM Description
\include{chapter2}

% chapter 3: 
\include{chapter3}
% chapter 4:
\include{chapter4}

% chapter 5:  
\include{chapter5}

% chapter 6: 
\include{chapter6}

% Chapitre  de conclusion (générale)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\include{chapter7}

% Liste des références bibliographiques
\printbibliography
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Début de la partie annexe éventuelle
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% \appendix
%
% Premier chapitre annexe (éventuel)
% \chapter{...}
% ...
% Deuxième chapitre annexe (éventuel)
% \chapter{...}
% ...
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Début de la partie finale
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\backmatter
%
% (Facultatif) Glossaire (si souhaité distinct de la liste des acronymes) :
% \printglossary
%
% (Facultatif) Index :
% \printindex
%
% Table des matières
\tableofcontents
%
% (Facultatif) Production de la 4e de couverture :
\makebackcover
%
\end{document}