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First, you should look at a document in the HealthStream Administrator Help titled "Edit, Version, or Copy a Course". It's on the Recommended Practices page, where you'll find a lot of helpful hints for all kinds of subjects.
We have 2 major training windows, so I update some of the courses in November/December for the January release and the rest in May/June for the July release. We have to get VP approval to add new courses to the company-wide assignments (department-specific courses just require director or manager approval--full disclosure, I'm only responsible for the company-wide assignments.)
In most cases, I reversion my courses to update them and republish them with an un-enroll/re-enroll. That should automatically put the currently-enrolled and yet-to-be-enrolled assigned students in the newest version (don't do this if it is a live class or you will lose all your currently registered people--the old class dates don't attach to the new version anyway). If the courses are in a curriculum, you'll have to republish the curriculum with an un-enroll/re-enroll, too. If the people who have already completed the old version need to take the new version immediately, I have to re-assign it. Otherwise, they'll get the new version in the next round of training. I like to reversion whenever possible because I don't have to retire the old version or change the assignments. There are some quirky exceptions to that based on how our system was originally set up.
There are times when you'll need to copy or create a whole new course. I would to publish and assign the new one first, then immediately inactivate the old assignment and un-enroll people, then retire the old course. If you retire it while the assignment is still in progress, you will get phone calls from people who can no longer access it and are "stuck". The timing will always be tricky with new hires. We have orientation every other week and most new hires finish their main assignments their first week, so I try to time around that. I often choose a line in the sand for new hires and don't un-enroll/re-enroll when I publish, so one group is in the old version and everyone else going forward is in the new version. This is usually timed around the January and July release dates. I also plan everything out before I do it, so I can make the changes quickly and it will affect the least number of people.
There are a lot of "If this, then that" decisions, but that would take too long to post. I'm sure this is not the only way to handle updates. If you have specific questions, you can reply to this or email me at email@example.com and I'll try to clarify.