% !TEX root = John1-w.tex
% John1-w.tex

\input {_header} 

\definingfootnotestrue        % or however the boolean is set true initially
\excludecomment{glossarytext}
\input {_glossary}

\begin{document}
\input{_BiblioRef}
\input{John1}

\definingfootnotesfalse       % <-- the missing piece
\includecomment{glossarytext}
\input {_glossary}

\end{document}