After an Administrator enables the assessments for particular jobs, you may have those applicants go back through the application process as usual. As long as the applicant uses the same identifiers they used previously, it will connect it to their current applications. If the applicant does not use the same identifiers, a new application will be created.
As a best practice, it is important to be consistent. You can enable or disable the assessments for a job but do not switch this setting off and on while applicants are applying.