I'm having the same issue for a few years now. Gah.

WOW. Someone PLEASE escalate this issue. I feel like we are all talking with a chatbot. (and not a very good reader at that) I'll restate the problem we are all having: 

Is there a way to have QB Desktop leave the check number blank for imported payroll checks?

Our payroll checks are all Direct Deposited, and show "DD" in the QB online payroll system, but that info is not passed to QB Desktop when exported payroll data is imported. I have to manually edit the number for each check (set to blank, or ACH, etc), so that the next check printed remains in the right sequence and there are no duplicated check numbers in the register.

It is clear that there is a problem with how QB desktop handles imported checks without check numbers. This should be a preference that is adjustable, or the check number field should be left blank until that check is printed. Not a hard fix. I dealt with this for YEARS before I thought to look here. I'm certain there are thousands of users like me who are incrementally annoyed by this bug. after enough bugs - we look for a better product.

THIS SHOULD BE ON THE TOP OF THE LIST OF BUGS TO FIX WITH THE NEXT UPDATE.

All imported Payroll "checks" are assigned check numbers. All are Direct Deposited so this screws up the check sequence and creates duplicates.

Hello there, @PPSKC.

I am aware of the benefits for businesses like yours. Like you, I want this feature to be in QuickBooks Desktop (QBDT).

But QBDT is still unable to get to it. However, I encourage you to engage with our software engineers about your ideas. They pay close attention to customer feedback, especially to make QuickBooks better.

Follow the steps below:

1. Go to the Help option.
2. Select the Send Feedback Online option.
3. Choose the Product Suggestion option. A pop-up window displays.
4. Enter your feedback suggestion.
5. Click the Send Feedback button. Feedback sent.

I found helpful articles for more details about the tasks you can do with iif files: 

• Improved IIF Import in QuickBooks 2019.
• Export or import Intuit Interchange Format (.IIF) files.

Let me know if you need further assistance working with QuickBooks. I’m always here to help. Have a good one!

Hi Ethal from Intuit,
You seem unaware this worked fine in QBDT until the 2019 or 2020 version of QBDT, at which point Intuit broke it. It's been three years now with multiple complaints, including from accountant users like myself who may have to deal with this in dozens of client files...

The way around it is to click the "I'll import it myself" option when bringing in IIF files, and ignore whatever dire warning QBDT throws onto the screen. That WILL bring in the transactions without erroneously assigning check numbers to direct deposits and tax payments.

And the way for Intuit's engineers to fix it, is to assign "DD" to the check reference field for direct deposit payroll entries when creating the IIF file, and "ACH" to the tax payments. Pretty easy-peasy so I really wonder why they haven't done that yet.

The way around it is to click the "I'll import it myself" option when bringing in IIF files, and ignore whatever dire warning QBDT throws onto the screen. That WILL bring in the transactions without erroneously assigning check numbers to direct deposits and tax payments.

This wasn't an issue until QBDT 2019 or 2020, when Intuit broke it. And the way for Intuit's engineers to fix it, is to assign "DD" to the check reference field for direct deposit payroll entries when creating the IIF file, and "ACH" to the tax payments. Pretty easy-peasy so I really wonder why they haven't done that yet.