If a student has been previously admitted through one account, but later applies (potentially as another student type) using a different account, their new application will need to be assigned to the initial Contact record that is associated with their M#. View the instructions for Re-Assigning an Application (PDF) on the right under Attachments.
NOTE: Just like any other duplicate (a student who has two Contact records), you will need to contact Recruiter support for their information to be merged after you've followed the steps listed in the above instructions.