Updating SCORM content to allow for students to retain progress depends if the IMSmanifest file has changed from the original publishing. If you overwrote the original file without changing the file name/structure it is possible that the imsmanifest file did not change and your student's progress will be retained.
Moodle and/or a plugin does not change the imsmanifest file.
Save a run of the student's current
activities status for a single course.
Backup the course within Moodle.
Make the changes to the content, do not change the file name or structure. Changing the name, such as; Math 101 V1.0 to Math 101 V1.1 will be a problem.
Replace the current content with the updated content.
Run the activities status report. See if they match.
If not, restore the original course.