ABC Amber CHM Merger is an advanced free tool that actually merges CHM files. The combined CHM doesn't depend on the source CHMs, so you can use and distribute it without needing source CHM files. The software supports more than 50 languages and can be run from a command line.
Important note: the program is able to merge CHM files that don't have a HHC (Table of Contents).
Partial Features List:
combines multiple CHM files into a single CHM file;
command line support;
easy to use and easy to set up;
saves and restores the list of documents to merge to;
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