Were the users enrolled onto the course via an "Audience Sync" enrolment plugin, or have they enrolled themselves via the certification? If it was the audience sync, I believe you should just be able to create a new one (attached to the new smaller audience) and then delete the old one (which should remove all assignments for the original audience).
If they enrolled themselves via the certification, it might be trickier because it doesn't appear possible to delete the Program enrolment method once it's part of the course (only disable it, which won't unenroll users fully).