We noticed our HST filings have not been properly marked in QBO as "record refund" or "record payment" for 2 years. Will this affect anything if we mark them all now?

Hello pmatchem-shinydo,

It's a pleasure to see you in Community.  Welcome!  QuickBooks Online tracks your sales tax payments and due dates so you can avoid late returns and extra fees.  Once you review what you owe, you're ready to file the return and record the payment information.  This ensures your sales tax payable remains accurate and up to date.

Although the Sales tax feature enables you to record your payments, you'll still need to submit payment to the CRA outside of QuickBooks.  However, since your sales tax filings date back to previous years, recording the payments could impact your books, if the associated accounts have been reconciled.  For this reason, I suggest speaking with an accounting professional for their expertise and best course of action, to ensure a positive impact on your books.  If you don't have an accountant, we can help you locate a ProAdvisor in your local area.

If you have any other questions, feel free to reach out.  We would be happy to help!