Hello there,
When you delete an invoice in QuickBooks Online, a warning appears stating, "This erases the invoice forever," and "You can't undo this." Deleting the transaction permanently removes it from your records.

Since you deleted the original invoice with the incorrect GST/HST, it no longer affects your sales tax tracking. When you create the new invoice with the correct tax settings, your Sales Tax Center will reflect the accurate amounts moving forward.
Moving forward, ensure you select Exempt or Out of scope instead of GST/HST since you didn't actually collect the tax.
If you catch a tax error on an invoice, edit it instead of deleting it. If you need to cancel the transaction entirely, void the invoice. Voiding keeps the record but zeros out the balance, strengthening your audit trail.
If you have further questions, don't hesitate to ask below; we're always here to help.