The Merge Module is a separate add-on to RoboHelp Office; therefore the Merge Module must be purchased and installed prior to merging WebHelp. In addition, See Also keywords are not merged in merged WebHelp systems.
According the RoboHelp.CHM:
If you generate using a skin, the skin from the master project will be displayed when users access the merged system. If users access the projects individually, the skin used in each project will be displayed.
If you generate using Traditional-style WebHelp (without a skin): Including a Show/Hide button in a sub-project may result in users losing access to the master project's TOC. If the user is viewing a topic in a sub-project and clicks the Hide button, then clicks the Show button, the sub-project's TOC will display instead of the master TOC.
If you merge WebHelp projects and the master project was generated using pure HTML or Section 508 compliant WebHelp, the sub-projects will only be available from the TOC (not from the index or full-text search). The sub-projects will appear as a book in the TOC. When users click the sub-project's TOC book, the sub-project will open in a new browser window.
Using a different project language in the sub-project is not recommended. If the sub-project has a different language specified, it will only be accessible through the TOC (the index and full-text search will be disabled) and end users will get an error message.
The master project must contain at least one index keyword that is associated with a topic or the index will be empty.