India follows Trade Date plus Two working days system for settlement from the exchange. If shares come short then they will come in the auction that is T plus 3.
In Back Office there is a report called 'Ultimate Delivery Report'. This report will inform you which shares are pending from Exchange and which one already gone in your Demat Account.
We never ever keep shares in our account overnight.
We allow our NRE and NRO Account to Buy Delivery Today and Sell Delivery Tomorrow at their own risk. They must be aware of the risk that if shares come short from Exchange subsequent sell will go in the auction and there will be penalty and losses which they have to bear.