Job switch and income tax

Hello, I have recently switched employer and my previous employer has asked me to submit the tax clearance certificate to release my final settlement. I had submitted the tax form in the LHDN office for the period of Jan 2016 to May 2016. I see I have received the tax refund amount from LHDN to my bank account today, close to whole amount of tax I have paid for the Jan - May 2016 period. 
So now,I am confused as to how should I submit for the income tax next year in April 2017 ?
I will be submitting for the whole assessment year 2016 - 2017 and how will LHDN calculate my tax again then ?.. Will they know that I had already received the tax refund for the Jan - May 2016 period ?.
Please help me understand this process..

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