With the exception of a limited number of graphics references, external files you reference in your template code are not automatically exported with your project because Help+Manual does not know about them. There are two ways to solve this problem:
Nowadays you will almost always choose an HTML skin to publish your project to WebHelp or HTML Help/CHM. A skin is a special kind of Help+Manual project without topics that only stores your HTML templates and all the settings relevant for HTML output to these two formats. When you choose a skin, the templates and settings in the skin completely replace those in your project.
Normally, a skin is pre-designed and you don't need to change anything. However, if you do want to change something, you must do all your editing in the .hmskin skin file. Editing in your Help+Manual project won't have any effect because those templates and settings are not used.
To edit a skin, make a copy of the .hmskin skin file in your project folder and then open it in Help+Manual by selecting .hmskin as the file type to open in the Open dialog. All the templates and settings are in the same places as in a normal Help+Manual project.
Exception: HTML Export Options
The HTML Export Options section is not stored in skins and needs to be edited in your project.