I submitted an invoice for works, submitted invoice with VAT. This invoice was paid late, and VAST submission already made, but the work was VAT exempt, can I recover?

Welcome to the Community space, @baileyplumbing.

Since the invoice was supposed to be exempted from VAT, you can adjust your VAT liability. However, it isn't possible to unfile a return that has been submitted to and approved by HRMC. QuickBooks Online follows the HRMC process that any adjustments that need to be made to a VAT return already submitted to will typically require you to make a subsequent VAT return.

It'd be best to contact HRMC directly for further clarification.

You can then refer to this guide on how to enter VAT adjustment in QuickBooks: VAT: Getting Started.

Keep me posted if you need anything else. I'm here if you have other questions or concerns.