There may be situations that you need to use same REFERENCE number for multiple invoices / Bills / Sales Receipts.

Normally our app warns when you tried to import using same REFERENCE Number. 

"Duplicate Document Number Error : You must specify a different number. This number has already been used "

To avoid this error, you need to enable  the option "Import Transactions with Duplicate Transaction Numbers (Invoice No,Bill No)" in Import Settings.

Though it allows you to import duplicate reference number, this impacts the overall speed of the import. So it may take little more than usual.