To remove a pupil from roll and mark them as archived, head to the Edit tab in the Pupil Profile.
From the School History area, select the 'Archive / Transfer via Leaver's Wizard' link:
This will take you to the Leaver's Wizard area with just the one pupil selected (denoted under the 'leavers selected' area):
Complete the fields and select 'Next' at the bottom of the page. If you also want to create a CTF, select the ;Generate CTF' button before selecting 'Next':
Finally, 'Confirm Leavers' in the resulting pop up to archive the pupil.
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