Vincent,

Nice to hear from you.  Let me apologize that I haven't been a contributer 
lately.  There are a lot of balls in the air here.

As to the question:  with this as test.tex

===== test.tex below ======
\documentclass[12pt]{article}
\includeonly{test1,
             test2}

\usepackage{lipsum}
\begin{document}
\include{test1}
\include{test2}
\end{document}
===== test.tex above ======


and these as test1.tex and test2.tex.

===== test1.tex below ======
\lipsum[1]
\label{ex:test1}
===== test1.tex above ======


===== test2.tex below ======
\lipsum[2]
\label{ex:test2}
===== test2.tex above ======

then running "pdflatex test" twice gives this.

ftpmaint@millstone:~/tmp/tex$ ls test*.aux
test1.aux  test2.aux  test.aux

The contents of those .aux files is what you would think.

ftpmaint@millstone:~/tmp/tex$ cat test1.aux
\relax 
\newlabel{ex:test1}{{}{1}}
\@setckpt{test1}{
\setcounter{page}{2}
\setcounter{equation}{0}
\setcounter{enumi}{0}
\setcounter{enumii}{0}
\setcounter{enumiii}{0}
\setcounter{enumiv}{0}
\setcounter{footnote}{0}
\setcounter{mpfootnote}{0}
\setcounter{part}{0}
\setcounter{section}{0}
\setcounter{subsection}{0}
\setcounter{subsubsection}{0}
\setcounter{paragraph}{0}
\setcounter{subparagraph}{0}
\setcounter{figure}{0}
\setcounter{table}{0}
\setcounter{lips@count}{1}
}


Regards,
Jim

------------------------------------------------------

If we pin this election on coastal elites, we are excusing white working-class 
and rural Americans for voting for a man accused of violating the Fair Housing 
Act by refusing to rent apartments to black people. If we pin this election on 
coastal elites, we are excusing white working-class and rural Americans for 
voting for a man who called Mexicans rapists, drug dealers and criminals. If we 
pin this election on coastal elites, we are excusing white working-class and 
rural Americans for voting for a man who called for a complete ban on Muslim 
immigration.

Patrick Thornton 
http://www.rollcall.com/im-a-coastal-elite-from-the-midwest-the-real-bubble-is-rural-america


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