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We do not advise overwriting SCORM courses within Fuse. Instead, we advise you to upload a new version of the SCORM course instead.
If you do choose to overwrite a SCORM course, then you can select the relevant option in Articulate Storyline and other WYSIWYG authoring tools, which ignores suspend data. This ensures that there are no issues when uploading a new version of a SCORM file, but it means that the users who are currently in progress must restart the SCORM course.