Malaysia multiple single entry visas allowed?

[bhoot960]

Indian here, I’m travelling to Indonesia via Kuala Lumpur for both onwards and return journey, I was of the assumption that my return journey is on same PNR so I don’t need a visa for Malaysia. So I got a single entry visa for my onwards journey, I now realise that my return journey is also on different PNR but same airlines. I leave in 3 days and return after a week. Can I apply for a single entry visa for the return now and use 2 single entry visa for my journey?