Wells Fargo and Quicken for Mac Bank Pay

Has anyone else had a problem with Wells Fargo processing of payments issued through Quicken for Mac using the Bank Pay option?
On February 15 I entered a payment to a landscaping service using Bank Bill Pay option the same way that I have done for 3 years. The only difference was this was a much larger payment than normal. The payment was assigned a four digit check number immediately and then cleared on my account on February 22 as an online payment with a 9 digit check number. On February 29 the owner of the landscaping service said he had not received the payment. I told him that it had cleared my account and we went back and forth a few times. As of March 4 he said his bank still had no record of a transfer for that amount. Wells Fargo said that they could retrieve the money and credit it to my account so that I could try again to send the payment, but they could not tell me where the money had actually gone. They also said it could sometimes take 10 business days after a transfer was debited from my account for it to show up in the payee's account. This means that a payment entered in Quicken can take over two weeks to actually reach the merchant. The person in the claims department at Wells Fargo said there may have been a "glitch" that caused the payment not to reach the payee's account.
The landscaping service seems to use Quickbooks. I do not understand how Wells Fargo can transfer money directly to a merchant's account unless they know the account number and routing number. Does Quickbooks share that information with banks so that it can receive electronic transfers?
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