As an update to an earlier post in this blog, the latest release of Chemdoodle contains changes to EPS export:
EPS output now includes an option to preserve chemnum tags in output. Such chemnum tags are defaulted as "TMPx", but you may change what the chemnum tag is to be used. These tags, when written in caption labels, will be preserved as unbroken text in EPS output, even if the Render Text as Shapes option is enabled. This way, you can work with chemnum and still have perfect font glyph output to EPS files for your figures.
Bitmap image output is now supported in EPS files.