I want to ensure this will be taken care of, @Threecountiesuk. I'm here to provide additional steps to help you file your CIS return in QuickBooks Online (QBO) seamlessly.
To start, let's check the status of your return on the CIS dashboard. When you filed via QBO, it normally takes up to 72 hours to update its status on the HMRC portal. However, those returns submitted through the HMRC Portal will not update the status in the program.
If you can't still see the return after the given time frame, I recommend reaching out to our Customer Care team to further check the root cause of the issue. They will also help you unfile the CIS return.
For more info about this, please check this article: File a CIS return in QuickBooks Online.
Keep me posted if you have any other concerns about filing your CIS return in QBO. I'm always here ready to back you up. Have a great day ahead.