Hi Annika,
That sounds similar to an issue we had where Totara archives the original course completion and the recertification course completion when the certification window opens in case the user doesn't complete the recertification course before expiry and therefore needs to recomplete the original course. This confused some of our users and would complete the original course when they should be completing the recertification course.
We got around it by not adding the original course to the certification and using an audience to enrol in the certification.
Our solution was: user completes course A and is placed in audience. Users in that audience are enrolled in the certification. The certification has course B as the content. When the window opens course B is reset but not course A.
Maybe that would worrk for you.
Regards,
Nathan