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Fly in and out of Singapore using Singapore passport. Fly in and out of Malaysia using Malaysia passport. For other countries make sure you are consistent i.e. you fly in and out of that country using the same passport (more likey you will use Singapore passport due to visa waivers except for Muslim countries where Malaysia passport may be more kosher (no pun intended).
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but if you depart changi airport using sg passport and go into malaysia using malaysia passport then if you return into sg , your sg passport will be clean no chop from malaysia so will not attract sg customs attention ?