Course chapters in one storyline file or seperate files for each chapter?

MariHijer​ : You should talk with your LMS folks about what options are available for combining SCORM packages. For example, many LMSs can combine multiple SCORMs into a "curriculum" (though they might use a different word for a given set of courses). 

A curriculum could be programmed in the LMS to require the user to complete all of the courses in order. Or to complete all of them in any order. Or to only require the user to complete one of the courses (For example, this may be done when each SCORM is a different language.) So the decision depends on your needs and on what the LMS can do.

As DavidTait​ said, a big consideration is how you want to track what a user does. You said they aren't required to complete every chapter.

If all of the chapters are combined in one Storyline file, you could run a completion trigger at the end of every chapter, so that the user would only need to finish one chapter to successfully complete the course. However, if the course is marked as complete after finishing one chapter, that could impact their access to it (depending on the LMS). And you wouldn't know what chapter(s) they completed.

As David also said, a bigger course could run into bookmarking problems. 

Bottom line: Based on the description, I think it's better to keep each chapter in its own Storyline file/SCORM package. Combine the SCORMS in whatever way the LMS allows that suits your requirements.