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I'll share additional details and troubleshooting steps about bill.com email notifications. This way, you'll receive email confirmations again.
Ensure that you're using your new Bill.com account so you'll receive the confirmation of your payment regularly. Using existing accounts will not be migrated to the Online Bill Pay service. This is because these are two different services offering distinct features. That could be the reason you're not receiving any notifications.
Check out this link for more details: Move from a Bill.com account to Online Bill Pay.
If this is the case, you must either cancel your Bill.com account or contact Bill.com to have your current Bill.com account disconnected from QuickBooks Online. After that, you'll be able to sign up for a Bill Pay account directly from QuickBooks.
Go as follows:
For more understanding about Online Bill Pay and Bill.com app features, check out the following links below:
If you need more explanation or instructions, don't hesitate to mention my name in the comment section. I'll do my best to answer every question you have about bills. I'll see you again soon.