keep the modified (tested) theory,
added an explicit reference to the modified theory in the generated log file
\documentclass[11pt,a4paper]{article}
\usepackage{isabelle,isabellesym}
\usepackage{pdfsetup}
\urlstyle{rm}
\isabellestyle{it}
\begin{document}
\title{Examples for program extraction in Higher-Order Logic}
\author{Stefan Berghofer}
\maketitle
\nocite{Berger-JAR-2001,Coquand93}
\tableofcontents
\parindent 0pt\parskip 0.5ex
\input{session}
\bibliographystyle{abbrv}
\bibliography{root}
\end{document}