In modular projects you also have to devote some thought and planning to topic IDs and context numbers. Modules are separate projects and Help+Manual can only prevent conflicts caused by duplicate IDs and context numbers within a single project. This means you are responsible for making sure that you do not have duplicates in the modules you are going to include in your help system.

See also:

Modular Projects (Reference)

IDs, Context Numbers and Keywords (Reference)