You need to replace the SCORM module (the .zip file) in the exact same SCORM activity. Do not create a totally new activity. In addition you must be certain the SCORM ID number in the manifest file is the same as the ID number in the module you are replacing. See the following:
How do you find out what the SCORM ID number is?
If the new SCORM package is just an update of the existing package, and it was modified using the same SCORM authoring tool, the ID will most likely be the same by default. However, if you created a totally new SCORM package or used a different authoring tool, then you will need to open the .zip file and edit some of the files;
See the following forum posts: