Updating SCORM package
You can always update a module in a course with another version by replacing the existing SCORM package. Here are the supported formats. Users who have already passed the course, won't have to redo it when a module is updated. The status is maintained at both the module level and the course level. If you were to remove a module, the user would maintain the course status, but there would be no record of the removed module in the statistics.
However, when the module is updated, the bookmark is removed and the users will not get the question to resume where they left off.