When Merchant Services receives payment all invoices should be and are marked "PAID". The problem is not all payments are posted to a cash account. Some payments post to the "Undeposited Funds" as they should, and others do not post to any cash account. So, when the Merchant Services Deposit is made to my bank and subsequently imported to QBO the deposit does not have a payment record to link to.
I'm determined to help you find the fix you're looking for, @CRM858.
As you noted, on certain occasions, batch payments processed through Intuit Merchant Services will be placed in Undeposited Funds instead of the Bank Account. This is usually the result of momentary server maintenance or one of the individual payments being unable to process immediately. The entire batch of payments will be sent to Undeposited Funds so you can group them together in a manual deposit to match with the transaction coming across the Bank Feed.
A Payment transaction, whether it's created manually or by Merchant Services, has to be posted to one cash account via the Deposit to field. You can locate the astray payments, re-assign their deposit account, and then batch them together however you need to link to the bank transaction. The steps below will help you accomplish this:
Locate the payment
From QuickBooks Online, navigate to the Sales tab > Customers tab.
Click the customer's name whose payment you're searching for.
The customer's transactions will appear below. Use the filter menu to narrow the list and find the payment.
Click the payment to open it.
Re-assign the deposit account
From the Payment transaction screen, click the drop-down under Deposit to.
If this payment was deposited by itself, select the bank/cash account. Otherwise, select Undeposited Funds so that you can create a batch deposit.
Click Save and close at the bottom.
Create the batch deposit
Click the Plus (+) icon and select BankDeposit.
Check off the payments that you'll be including in this batch deposit. You may have to click QuickBooks Payments to expand the section that holds Merchant Services payments.
Once finished, click Save and close at the bottom.
This will give you total control over your customer payments and allow you to deposit them in a way that will link with the imported bank transaction. Please don't hesitate to keep in touch with me here for all of your QuickBooks needs, I want to ensure your success. Thanks for coming to the Community, wishing you a wonderful weekend ahead.