I am trying to keep the students that have already been enrolled in sections, but even if I unmark the 'Clear enrollments before scheduling students in sections' checkbox on the Student Schedule page, they are being cleared out anyway.
We are currently evaluating this issue and will update this article when we have more information.
Steps to Duplicate
Navigate to onRecord > Procedures > Schedule Maker
Select the applicable School Year and School Level from the filters
Click on the Start Student Schedules Here button
Unmark the 'Clear enrollments before scheduling students in sections' checkbox that is located in the region labeled, "What should happen with existing enrollments?"