Here's a MWE using tikzmark to draw an arrow connecting two sub-nodes in a tree:
\documentclass{article}
\usepackage{tikz}
\usetikzlibrary{external}
%\tikzexternalize
\usetikzlibrary{tikzmark}
\begin{document}
\begin{tikzpicture}
\node {A}
child {node {\subnode{end}{B}}}
child {node {C \subnode{start}{B} E}};
\end{tikzpicture}
\begin{tikzpicture}[
remember picture,
overlay]
\draw[->] (start.south) to [out=south west,in=south east] (end.south);
\end{tikzpicture}
\end{document}
As expected, this yields the following output (calling pdflatex with -shell-escape):

However, if %\tikzexternalize is un-commented, compilation fails, with the following error:
! Package pgf Error: No shape named start is known.
Are tikzmark and tikz externalize incompatible? If so, are they fundamentally incompatible?
Edited to add: if fundamentally incompatible, is there any alternative way to execute something like the image in this post -- that is, to target a sub-node with (e.g.) an arrow?
\drawcommand to be part of a differenttikzpicture? It ought to work if you put it as part of the original one. – Andrew Stacey Jul 15 '15 at 22:59A). – SEC Jul 15 '15 at 23:02tikzmarkrelies on multiple compilations. Maybe there is a way around it, but I now always disable externalisation for pictures which usetikzmark. – cfr Jul 15 '15 at 23:24\subnodeand if it were going to work at all, it would presumably be in that case. (Because the later commands are part of the same picture.) – cfr Jul 16 '15 at 13:01\subnode? – cfr Jul 16 '15 at 13:02\includegraphicsing them into the master document? – Andrew Stacey Jul 16 '15 at 18:13