Data saving problem using frappe.ui function

If you want to set the value of is_late before_save then use before_save.

on submitting record use after_save or on_submit trigger 's.

use frm.set_value("field_name","value") instead of frm.doc.is_late=‘Yes’

My Recommendation to you is call validating_late_status function on the before_save trigger.
It may help you to solve your query.

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