Das Internationale Forum TeX Stack Exchange hatte [einen guten Tip](http://tex.stackexchange.com/a/235707) von [SoundOfSilence](http://tex.stackexchange.com/users/31729/soundsofsilence) parat. Hier meine daraus angepasste Lösung. DANKE!
======== Main.tex==========
\documentclass[12pt,a4paper]{book}
\usepackage[utf8]{inputenc}
\usepackage[german]{babel}
\newcommand\shortlabelprefix{short}%
\newcommand\longlabelprefix{long}%
\begin{document}
\newcommand\labelprefix{\shortlabelprefix}%
\input{kapitel}
\begin{appendix}
\newcommand*{\LONGVERSION}{}
\renewcommand\labelprefix{\longlabelprefix}
\include{kapitel}
\end{appendix}
\end{document}
======== kapitel.tex==========
\chapter{This is a chapter}\label{\labelprefix::chap:mychapter}
This is a test with a reference to my chapter \ref{\labelprefix::chap:mychapter}
\ifdefined\LONGVERSION
\section{Variant LONG}
This is a long version of the chapter, which contains a lot of additional information. This shall be placed in the appendix.
\else
\section{Variant SHORT}
This is the short version.
\fi
