A very long time ago (in computer years) when shelves of manuals were being converted to PDF or some other electronic file format, the concept of a "book" was maintained out of convenience (as in, "it's inconvenient for us to retypset all these books, so let's just convert the files to Microsoft Help and roll with it.")
It's been a long time since I've seen a company do that, or even need to do that. Today, online help is frequently contextual. In other words, if you strike the F1 key you receive help appropriate for what you're doing, not just the entire help file. Companies are doing this both to make obtaining help more intuitive for the user and to minimize the need to collate and present information as large blocks.
That was a very lengthy way of saying, whether you choose to use "chapter" or "section" has more to do with how you're presenting information to the user than the vehicle used to present it — and you didn't explain that aspect of your presentation.
I've been a programmer and technical writing for eons. My recommendation is that you avoid using the word "chapter." If you're creating the help correctly, it doesn't even make sense to use the word "section." The most common word to use is "topic" because while information may be available in a block context "start with the introduction and start reading," online help is used far more often with a search engine, which doesn't return a list of sections, it returns a list of topics (from a programming/technical writing perspective).
If this answer failed to meet your needs, please provide more information about how you are organizing your information and your intended user model.