As you write documentation, you will no doubt write passages that you don't want included in the accompanying online Help file. Likewise, some content may be appropriate for the Help file but not the written documentation. You may even have content that you want targeted at specific audiences. Yet, if you are looking for the ease of single-source Help authoring, making separate files for each platform would defeat this entire concept.
There's a better solution: Doc-To-Help lets you mark text, graphics, whole topics, or entire documents to be included in or excluded from either the manual or any combination of online Help platforms using the conditional text and attribute features.
More:
Conditional Text Target Options
Working with Conditional Text in Word Documents
Working with Conditional Text in HTML Documents
Applying Multiple Conditions to Text
Applying Conditional Text to a Topic