Tienes que repetir el WHERE cláusula, solo se aplica a un SELECT consulta, no la UNION completa .
SELECT a.id_skd as idab,a.nl as nl1, a.aa as aa1,a.jp as jp1, a.syarat_lampiran as syarat_lampiran1,a.riwayat_kelola as riwayat_kelola1,a.notifikasi as notifikasi1
FROM skd a
WHERE notifikasi = '1'
UNION ALL
SELECT b.id_skb as idab, b.nl as nl1, b.aa as aa1, b.jp as jp1, b.syarat_lampiran as syarat_lampiran1,b.riwayat_kelola as riwayat_kelola1, b.notifikasi as notifikasi1
FROM skb b
WHERE notifikasi='1'
ORDER BY riwayat_kelola1 DESC
LIMIT 1
