Client wants .story (unpublished files) - do they need this?

I have no problems with that, my clients get the source files at the end of every project. I have no reason to be protective of my content that was developed for them. As far as IP is concerned I have a contract that indemnifies me.

What the client does with the source files after they are handed over is beyond my control and I do not worry about it.  I am sure I have said above that I hope I add more value to a clients business than just delivering a course/module.  I would hope that same client would want to come back to me because of this, if they do not, I don't want to make it any difficult for them to use another freelancer/developer/instructional designer.

I costs include the source files being handed over, there is no reduction if they don't want them.

I think one of the issues/problems here is that people in our industry get emotionally attached to their files  or are frightened that someone will come along and steal their breakfast, the key thing to look at is what value do you bring to the table, and it is that which will keep the client coming back for more.