Hi Tanya,
I think if you just change the names of the courses this should present no issue.
Also, if you are changing the SCORM file, as long as you don't delete the old SCORM activity and just change the SCORM file on the activity that should be equally OK. For example, if you have an annual certification for which the stakeholder is happy to just change the SCORM every so often, then, as far as completion tracking goes, it will have an effect only on the users who are yet to (re)certify as they will have to pass the new SCORM. For the users who already certified, nothing should change.
One of the things which would help me decide on the approach with similar change is what my stakeholders expect the certification completion to show after the changes have been implemented.
To illustrate my point I'll suppose that it's an annual certification. So, if somebody completed the certification day before you are to make the necessary changes, what would be the expectation of your stakeholders? Is this person certified for another year or would they like this person to be Not certified and expected to complete the courses once again?
If the former is their answer, you have no problem :)
Best,
Vlad