I understand how important to import the reference number of your transactions inside QuickBooks. Currently
As a workaround, you can manually update each transaction to enter the Reference number. You can use the Custom transaction numbers feature to set your numbering preference.
Here's how:
Go to the Gear icon.
Choose Account and Settings.
Select Sales, then click anywhere within the Sales form content section.
Check the box next to Custom transaction numbers.
Select Save and then Done.
Open an invoice or any sales form, and in the Invoice no. field, enter the custom number or letter sequence you want to use for your forms.