I ran into the problem that in my .eps files generated via ChemDraw 16.0 do not get their tags replaced. I tried using a .eps file from 2 years ago (because back then everything worked fine) and for this file it worked.
So I generated the same file twice, once using ChemDraw 16.0 and once using Chemdraw 15.0 and only the latter worked.
This is the code I used:
\documentclass[
a4paper, %% DIN A4-Papier
DIV=calc, %% Satzspiegel berechnen
11pt, %% Schriftgröße
captions=tableheading, %% Tabellenüber- statt unterschriften
english%,german,ngerman %% deutsch als Dokumentsprache, Englisch als zusätzliche
]{scrreprt} %% KOMA-Skript Report als Klasse
\usepackage{graphicx}
\usepackage{hyperref}
\usepackage{chemnum}
\usepackage{auto-pst-pdf}
\begin{document}
\begin{figure}
\centering
\replacecmpd{cmpd:1}
\replacecmpd{cmpd:2}
\replacecmpd{cmpd:3}
\includegraphics[width=1\textwidth]{ChemDraw/CHI-014-CD15.eps}
\end{figure}
\begin{figure}
\centering
\replacecmpd{cmpd:1}
\replacecmpd{cmpd:2}
\replacecmpd{cmpd:3}
\includegraphics[width=1\textwidth]{ChemDraw/CHI-014.eps}
\end{figure}
\end{document}
EPS File generated with Chemdraw 16.0
Can anyone imagine why this occurs or help me out so I can also use ChemDraw 16.0?

By the way somebody else already posted that Error back in January here on the PerkinElmer Support Forum
– Christoph H. May 24 '17 at 20:11