HI Kevin,
I agree with the thought of setting up a new Certification. If I'm understanding the workflow right, what you could do is create the new certification, with the appropriate completion criteria and then import the completion data from the old certification. That way you get the new completion requirements, with the last completion dates. (Though if the courses were through Totara, it would automatically look at the completion dates of those courses and apply them to the new certification.) With the custom script in there though, you'll want to go back to your Totara Partner to talk through it, just in case there's some piece I'm missing.
Thanks!
Wes