A SCORM course holds data about a user's progression and when it loads, it validates this data against the imsmanifest.xml file. If the data does not match, an error will occur. For example, if you originally had 14 slides in a SCORM course and you remove 1 slide, the data will no longer match, as the expectation is, there are 14 slides in the SCORM course.
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 with uploading a new version of a SCORM file, but it will mean that the users who are in progress will have to restart the SCORM course.