We are currently evaluating this issue for a fix in a future release or patch.
Steps to Duplicate1. Go to Scholarship module\application history
2. Find the scholarship application in question
3. Open the scholarship application and go to the Adjustments tab
4. Run the Scholarship Adjustments Process and click the Refund radial button
5. Enter in the refund amount for multiple payment lines, and process the refund.
6. See that only one line was affected by the refund.