Custom LMS behavior updating to HTML5

We are in the process of replacing all of our Flash reliant published courses with HTML5 only published courses.

In the past we had a need for a custom quiz that remained in the user's enrollment on our LMS until they had answered all the questions. Then once they had answered all the questions it would pass or fail them based on their score. This allowed busy workers to take part of the quiz, quit, comeback take some more, and so on, without failing.

This all worked great for Flash reliant content.

Once we updated to HTML5 only publish our modified javascript (which was in the lms.js file) didn't run anymore and we are trying to figure out a replacement.

It seemed like it would be easy to figure out why our HTML5 only versions fail them if they close the course in the middle of the quiz, but we can't figure it out.

Has anybody else done anything like this? How can we not evaluate the user's quiz results until they have actually answered all the questions?