Advice on an efficient method to strip out color tags from LaTeX
The option
\usepackage[monochrome]{color}
was designed for that use.
This does not solve your current problem (David's answer should work fine in this respect).
However, next time you need to highlight changes for your editor, remember that LyX has a pretty good built-in change tracking system: Just do your edits in change-tracking mode and you are done:
It's possible to have mark-ups for the changes in the PDF output, however, this is optional, so you could always also generate a plain PDF:
Once you are finished, or if you editor has already approved some of your edits, you can make them "permanent" by accepting the respective change in LyX.
I have used this process in for a couple of journal and shepherded conference papers. The respective editors were always extremely happy with the highlighting