\documentclass{beamer}
\usepackage{listings}
\usepackage{tikz}
\usepackage{pgfplots}
\usetikzlibrary{positioning,arrows,tikzmark}
\usetheme{Darmstadt}

\begin{document}

\begin{frame}[fragile]
    \frametitle{Codestructure sample modification}

    \begin{tikzpicture}[overlay, remember picture, thick]
      \only<1>{\node (a) at (0,1) {\phantom{A}};}
      \only<2>{\node (a) at (0,1) {A};}
      \only<1>{\node (b) at (0,3) {\phantom{B}};}
      \only<2>{\node (b) at (0,3) {B};}
      \draw [->] (a) -- (b);
    \end{tikzpicture}

\end{frame}

\end{document}