Here is a proposal to solving your problem. The short-version of your article would have the same environments as in the long-version, with an additional optional argument. The optional argument is the long-version label (referenced as an external file via the xr package). This argument is assigned to the short-version environment counter to correct for removal of similar previous environments.
Consider, for example, this is your long-version article (called long-article.tex, say):
\documentclass{article}
\usepackage{lipsum,ntheorem}%
\newtheorem{theorem}{Theorem}% Theorems
\newtheorem{lemma}{Lemma}% Lemmas
\newtheorem{proposition}{Proposition}% Propositions
\begin{document}
\section{Introduction} \lipsum[1]
\begin{theorem} \lipsum[2] \label{thm:first} \end{theorem}
\begin{lemma} \lipsum[3] \label{lem:first} \end{lemma}
\section{Definitions} \lipsum[4]
\begin{theorem} \lipsum[5] \label{thm:second} \end{theorem}
\begin{proposition} \lipsum[6] \label{pro:first} \end{proposition}
\section{Methodology} \lipsum[7]
\begin{theorem} \lipsum[8] \label{thm:third} \end{theorem}
\begin{proposition} \lipsum[9] \label{pro:second} \end{proposition}
\lipsum[10]
\begin{lemma} \lipsum[11] \label{lem:second} \end{lemma}
\section{Conclusions} \lipsum[12]
\begin{theorem} \lipsum[13] \label{thm:fourth} \end{theorem}
\end{document}
Now you create a short-version article (called short-article.tex, say):
\documentclass{article}
\usepackage{lipsum,ntheorem,xr,ifmtarg}
\newtheorem{shorttheorem}{Theorem}% Theorems
\newtheorem{shortlemma}{Lemma}% Lemmas
\newtheorem{shortproposition}{Proposition}% Propositions
\externaldocument[long-]{long-article}% Long-version article
% (SHORT) Theorem definitions
\makeatletter
\newenvironment{theorem}[1][]% Short-version theorems
{\@ifnotmtarg{#1}{%
\setcounter{shorttheorem}{\ref{#1}}%
\addtocounter{shorttheorem}{-1} \vspace{-\baselineskip}}%
\begin{shorttheorem}}%
{\end{shorttheorem}}%
\newenvironment{lemma}[1][]% Short-version lemmas
{\@ifnotmtarg{#1}{%
\setcounter{shortlemma}{\ref{#1}}%
\addtocounter{shortlemma}{-1} \vspace{-\baselineskip}}%
\begin{shortlemma}}%
{\end{shortlemma}}%
\newenvironment{proposition}[1][]% Short-version propositions
{\@ifnotmtarg{#1}{%
\setcounter{shortproposition}{\ref{#1}}%
\addtocounter{shortproposition}{-1} \vspace{-\baselineskip}}%
\begin{shortproposition}}%
{\end{shortproposition}}%
\makeatother
\begin{document}
\section{Introduction} \lipsum[1]
\begin{theorem} \lipsum[2] \label{thm:first} \end{theorem}
%\begin{lemma} \lipsum[3] \label{lem:first} \end{lemma}
\section{Definitions} \lipsum[4]
\begin{theorem} \lipsum[5] \label{thm:second} \end{theorem}
\begin{proposition} \lipsum[6] \label{pro:first} \end{proposition}
\section{Methodology} \lipsum[7]
%\begin{theorem} \lipsum[8] \label{thm:third} \end{theorem}
\begin{proposition} \lipsum[9] \label{pro:second} \end{proposition}
\lipsum[10]
\begin{lemma}[long-lem:second] \lipsum[11] \label{lem:second} \end{lemma}
\section{Conclusions} \lipsum[12]
\begin{theorem}[long-thm:fourth] \lipsum[13] \label{thm:fourth} \end{theorem}
\end{document}
You only need to add an optional reference argument to those environments following a removed one ('lemma' and 'theorem' in the above example).
I am not sure why additional (vertical) space was added after executing the \setcounter and \addtocounter commands. However, that's why a negative \baselineskip was added to correct for this behaviour.
xrpackage in order to reference an external document - the long-version of your paper in this case. Consequently feed the long-version's labels to each of the short-version environments. – Werner Jul 16 '11 at 06:17