OK well we have ascertained that it definitely is a SCORM package you need to upload. I am going to move this to the SCORM forum so you can get more specific help. I can't say why you are getting such an error message about not being able to delete a module instance when uploading but there are some SCORM error messages I'm not familiar with.
EDIT.. also - I have found some SCORM issues with that error, and they suggest the actual building of the package might be incorrect. See https://moodle.org/mod/forum/discuss.php?d=269123#p1161741 for example. I wonder if each chapter should be uploaded separately as a separate (but still zipped) folder? Can you try just adding one of the chapters in the same way as before?