I have submitted a pay run to HMRC but it is incorrect.I know how to unlock and delete a pay run but does that update with HMRC once I delete it within QBO

Yes, it will update HMRC and it will also delete the corresponding FPS (Full Payment Submission), @simon92. Let me share more details below about the things you should consider before deleting the pay run.

Here are the following:

• Deleting a pay run is permanent and cannot be undone.
• Deleted pay run information cannot be recovered or retrieved.
• Any HMRC notices or tax code changes that were applied will need to be reversed manually.

Additionally, if you need to modify the previous pay run, unlock the period and make the necessary adjustments. You don't need to run the payroll in sequence, as the figures will automatically update along with your Full Payment Submission (FPS) when you return to the current period. Here's an article for more details: Delete or unlock payroll in QuickBooks Online Advanced Payroll and QuickBooks Bureau Payroll.

For a comprehensive overview of payroll activities across multiple runs, you can access the Consolidated Payroll Reports. Check out this article for more details about the available reports in QBO Payroll Advanced: Run payroll reports in QuickBooks Online Advanced Payroll.

Keep me posted for clarification about managing pay runs in QuickBooks or other payroll concerns. We're always here to help.