You will have entered the Phonics results at Admin > Students > Statutory Assessments (or Workspace > Statutory Assessments if this is set up from the Teacher Dashboard).
In order to delete marks you will need to select End of Key Stage One from the dropdown in this area (instead of Phonics).
Highlight the two Phonics assessments in green (click and drag your mouse or hold down the control key whilst selecting both). Put the Curriculum Year as 1 or 2, depending on their current year group. Press Choose in order to bring up the table of students with their results. From the dropdown you can find Remove as an option at the top of the marks list. Once the mark has been removed, Save at the base of the page. The mark will now have been removed from the student's record.