Once you've checked in a returned loan, and marked them all accounted for in the database (and filled in the date closed!) you can now run the necessary reports.
From the reports tab, select the NPL Loan Invoice. A query interface will pop up (it's slow, don't worry- that's normal). Set the role to borrower (or Sponsor, if the borrower is a student) and enter the loan number in the correct field.
Hit OK, and the report generator will launch.