To update an existing SCORM unit by uploading a new SCORM file, either click on the unit's "Edit" (1) button in the course's "Dashboard" or hit the "Edit Unit" (2) button in the unit's page.
When your new content is uploaded, there's a new option in the unit's settings called "Reset suspend data" (1).
That option allows you to decide whether the users' progress in the SCORM unit is preserved or they have to start from the beginning:
Activate the "Reset suspend data" option to reset the users' progress in the updated SCORM content. That is useful when bookmarks in the SCORM content have changed. All progress made by users in their previous visit is lost and, when they return to the unit, they have to start over.
Leave it unchecked (as it is by default) when bookmarks in the SCORM content haven't changed, and you want the user to decide whether to resume from where they last left the unit or reset their progress and start from scratch (by answering "Yes" or "No" in the respective pop-up question).