Cheque in Hand

My company has received some share applications in Cash. But due to Income Tax issues, I refund the cash and I ask the parties to give me cheques. Due to it being year end I am in no mood to encash the cheques now. However, I am ready to allot shares based on such "cheque in hand"? How prudent is my decision from ROC as well as Income Tax point of view?

Should I retain some cash application and allot shares based on partly cash and partly cheque application. Pls advise.