@msantos good evening to you.
This may be a pain? But is leveraging two courses per certification an option for you?
The thing I am thinking is to support those people with certification waivers? You put them into a flavor of a course called course name - waiver and mark their enrollment as completed - you then deliver a different certificate to them.
Where that may cause significant types of work - you may be able to leverage validity for the course as a way to expire out the waivers and have that on the certificate.
You would never put the course waiver course in a catalog or anything like that. And you only allow admins to enroll people into them.