Thank you for posting in the Community, @AYH-RandyA. I'll provide helpful information about disabling main bank in QuickBooks Online (QBO).
Disabling the sync between the main bank account and QBO should not affect QuickBooks' ability to auto-withdraw payroll taxes, as long as the necessary bank account information for payroll processing remains active in QuickBooks Payroll settings.
Additionally, you may find this article helpful; it explains how to change your company's bank account for payroll: Change your payroll bank account.
Furthermore, you might find it beneficial to read this article, which discusses different types of payroll contacts and how to update them: Change your primary principal, payroll admin, or other payroll contact.
If you require further assistance with managing your payroll or have any other QBO-related concerns, I'm always here to help. Have a great day.
