Highlight and use arrows in an equation In a robust manner

I don't quite understand the output you have in mind, but I definitely would go through the tikz matrix way, by putting two matrices of nodes in the same tikzpicture, without using remember picture nor overlay.

For example:

\documentclass{article}
\usepackage{amsmath, amssymb}
\usepackage{tikz}
\usetikzlibrary{arrows,matrix,positioning}% For nice arrow tips
\begin{document}

\tikzset{
    !/.style = {
        fill=yellow!30,
    },
    mymatrix/.style = {
        matrix of math nodes,
        left delimiter  = (,
        right delimiter = ),
        nodes={minimum width=6ex},
    }
}

\begin{tikzpicture}
    \matrix[mymatrix, name=M1]{
                1 \\
        |[!]|   2\rho\pi \\
        |[!]|   3\\
    };
    \matrix[mymatrix, name=M2, below=of M1] {
                 1 \\
                 2\rho\pi\\
        |[!]|    3\\
    };
   \draw [red, >=stealth, <->, shorten <= 3pt, shorten >=3 pt]
     (M1-2-1.south east) to[bend left=60] (M2-3-1.east);
\end{tikzpicture}

\end{document}

Produces:

Result


By means of hf-tikz, one isn't forced to exploit the TikZ-matrix. This is an example showing how to perform such a task:

\documentclass[11pt,a4paper]{article}
\usepackage{amsmath, amssymb}
\usepackage[customcolors,markings]{hf-tikz}
\usetikzlibrary{calc}

\tikzset{aspect/.style={
    set fill color=green!50!lime!60,
    set border color=white,
    disable rounded corners=true
  },
  vert offsets/.style={
    above offset=0.32,
    below offset=-0.08
  },
  expr/.style={
    left offset=-0.05,
    right offset=0.25,
    vert offsets,
    aspect,
  },
  number/.style={
    left offset=-0.1,
    right offset=0.1,
    vert offsets,
    aspect
  }
}

\begin{document}
\[\begin{bmatrix}
     1 \\ \tikzmarkin[expr, mark at=0.135]{a}2\rho \pi \\ 3\tikzmarkend{a}
\end{bmatrix}
\]
% store the point in a coordinate: let it be a bit shifted for clarity
\tikz[remember picture,overlay]\coordinate[use marker id,xshift=0.1cm] (A) at (0,0);

\[\begin{bmatrix}
     1 \\ 2\rho \pi \\ \tikzmarkin[number, mark at=0.135]{b}3\tikzmarkend{b}
\end{bmatrix}
\]
% store the point in a coordinate: let it be a bit shifted for clarity
\tikz[remember picture]\coordinate[use marker id,xshift=0.25cm] (B) at (0,0);

% draw the curve
\tikz[remember picture,overlay]\draw[blue] 
 (A) edge[bend left=60,stealth-stealth](B);
\end{document}

The result:

enter image description here

The markings option is a feature of version 0.3 of the package, highly based on the nice answer Jake gave in How to draw tangent line of an arbitrary point on a path in TikZ. It exploits the TikZ markings library, thus it is possible to deploy markers as a number from 0 (start of the path) to 1 (end of the path). To show where the markers are placed, use the show markers key; for example:

\[\begin{bmatrix}
     1 \\ \tikzmarkin[expr, show markers, mark at=0.135]{a}2\rho \pi \\ 3\tikzmarkend{a}
\end{bmatrix}
\]

...

\[\begin{bmatrix}
     1 \\ 2\rho \pi \\ \tikzmarkin[number,show markers, mark at=0.135]{b}3\tikzmarkend{b}
\end{bmatrix}
\]

gives:

enter image description here

Moreover, the package allows to define aspects style in terms of shading: they can be adopted separately each time one highlights a formula. One way to use them, is the following:

  • define some general aspects style, say aspect x;
  • define styles containing offset definition plus an argument: this will be in charge to select the proper aspect style; an example: expr=aspect x.

This is an example covering some of the possibilities:

\documentclass[11pt,a4paper]{article}
\usepackage{amsmath, amssymb}
\usepackage[customcolors,shade,markings]{hf-tikz}
\usetikzlibrary{calc}

\tikzset{aspect 1/.style={
    set border color=green!70!black,
    top color=white,
    bottom color=green!50!lime!60,
    disable rounded corners=true
  },
  aspect 2/.style={
    set border color=cyan!50!blue,
    bottom color=white,
    top color=cyan!50!blue!60,
    disable rounded corners=true
  },
  aspect 3/.style={
    set border color=white,
    inner color=white,
    outer color=red!75!black!30,
    disable rounded corners=true
  },  
  vert offsets/.style={
    above offset=0.32,
    below offset=-0.08
  },
  expr/.style={
    left offset=-0.05,
    right offset=0.25,
    vert offsets,
    #1,
  },
  number/.style={
    left offset=-0.1,
    right offset=0.1,
    vert offsets,
    #1
  }
}

\begin{document}
\[
\begin{bmatrix}
     1 \\ \tikzmarkin[expr=aspect 1, mark at=0.135]{a}2\rho \pi \\ 3\tikzmarkend{a}
\end{bmatrix}
% store the point in a coordinate: let it be a bit shifted
\tikz[remember picture,overlay]\coordinate[use marker id,xshift=0.1cm] (A) at (0,0);
\hspace{1cm}
\begin{bmatrix}
     1 \\ \tikzmarkin[expr=aspect 2, mark at=0.135]{a2}2\rho \pi \\ 3\tikzmarkend{a2}
\end{bmatrix}
% store the point in a coordinate: let it be a bit shifted
\tikz[remember picture,overlay]\coordinate[use marker id,xshift=0.1cm] (A2) at (0,0);
\hspace{1cm}
\begin{bmatrix}
     1 \\ \tikzmarkin[expr=aspect 3, mark at=0.135]{a3}2\rho \pi \\ 3\tikzmarkend{a3}
\end{bmatrix}
% store the point in a coordinate: let it be a bit shifted
\tikz[remember picture,overlay]\coordinate[use marker id,xshift=0.1cm] (A3) at (0,0);
\]


\[
\begin{bmatrix}
     1 \\ 2\rho \pi \\ \tikzmarkin[number=aspect 3, mark at=0.135]{b}3\tikzmarkend{b}
\end{bmatrix}
% store the point in a coordinate: let it be a bit shifted
\tikz[remember picture]\coordinate[use marker id,xshift=0.25cm] (B) at (0,0);
\hspace{1cm}
\begin{bmatrix}
     1 \\ 2\rho \pi \\ \tikzmarkin[number=aspect 1, mark at=0.135]{b2}3\tikzmarkend{b2}
\end{bmatrix}
% store the point in a coordinate: let it be a bit shifted
\tikz[remember picture]\coordinate[use marker id,xshift=0.25cm] (B2) at (0,0);
\hspace{1cm}
\begin{bmatrix}
     1 \\ 2\rho \pi \\ \tikzmarkin[number=aspect 2, mark at=0.135]{b3}3\tikzmarkend{b3}
\end{bmatrix}
% store the point in a coordinate: let it be a bit shifted
\tikz[remember picture]\coordinate[use marker id,xshift=0.25cm] (B3) at (0,0);
\]


% draw the curve
\tikz[remember picture,overlay]\draw[cyan!50!blue] 
 (A) edge[bend left=60,stealth-stealth](B);
\tikz[remember picture,overlay]\draw[red!75!black] 
 (A2) edge[bend left=60,stealth-stealth](B2);
\tikz[remember picture,overlay]\draw[green!70!black] 
 (A3) edge[bend left=60,stealth-stealth](B3);
\end{document}

The result:

enter image description here