Renewal Application of EP is returned back due to expired EP

MY EP has expired from 2 days and when company applied it is rejected as it should be valid EP for at least 1 month . SO what is the action now as also my Visa expired yesterday and now I am staying with no valid visa inside malaysia . Is this a problem for me?? How they can renew the EP in this case for another 1 year as per my new contract with the company??
Also for the visa expiry , Do I have to go out from the country and come back for Visa expiry issue??

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