Removing make up credits from an account is a simple process. Make-up credits show up as packages on the student's profile.
Open the student's profile and go to the Packages tab. Find the make-up credit and click Action > Update Credit Count (or Update Credits).
The Edit Package Count pop-up shows the Total Count and the Used Count. Set Update Available Count to the number of unused credits you want the student to keep. Set it to 0 to remove all unused make-up credits. Credits that have already been used can't be removed this way.