@wale this fields are created from patch execution and this only gets executed once.
you can try to re-execute it from your bench itself
bench --site yoursitename execute hrms.patches.v1_0.rearrange_employee_fields.execute
bench --site yoursitename execute hrms.patches.v14_0.create_custom_field_in_loan.execute
same way other patch you can find here https://github.com/frappe/hrms/blob/version-14/hrms/patches.txt
Give it a try ! this might fix your field creation issue