Yes, you can partially convert your E-Margin position to delivery however, on T day, if you need to convert an E-margin trade to delivery; the quantity should to be equal to the executed quantity at trade level.
For example, you placed a buy order for 100 INFOSYS shares. The order got executed in parts: 40, 30, 20, and 10 shares with four trade reference numbers. Now, if you wish to convert this trade to delivery, you can do so based on the quantity in each trade reference number. Now if you try to convert 50 shares on 'T' to delivery in one go, system would not allow you to do so.
From T+1 Day to T+90 Days , you can convert E-Margin Open Positions to delivery as per your requirement.