How you create links between modules depends to a great extent on whether you use runtime or publish time merging. If you use publish time merging all the modules are always present so you can use normal topic links. If you use runtime merging for CHM files (it is only supported in CHM) you should use the A-link method (see below) for all links to modules which might not be present at runtime.
•Remember that runtime merging is only possible in HTML Help (CHM) help files. All other formats use only publish time merging.
•Even with runtime merging, links from child modules to the master module are always OK because the master module is always present.
•It is better to use A-links for all links from the master to child modules and between child modules for runtime merging projects. Then you can always be sure that you will not have problems if you ever need to leave a module out.
•External windows cannot be used across module boundaries in modular help with HTML Help. You cannot make a link that opens a topic from another help file in an external window. This is a restriction of HTML Help.
Modular Projects (Reference)