A costumer disputed some charges the job was done

I know a way on how to handle this in QuickBooks Online, MRPERFORMANCE. 

When a payment gets disputed, don't issue a credit to your customer’s card or any other type of refund. I'm here to show you the correct process.

Once a customer disputes a charge, the financial institution notifies QuickBooks Payments. Then, QuickBooks checks for the credits when receiving the disputed payment. I've listed below the cases where we can't match the payment to the credit: 

• If the sale and refund amounts are different.
• If you issue a credit to the card after the dispute has already been posted to your account. If this happens, send a copy of the credit issued to the card or proof that a refund was given (such as the front and back copy of the cashed refund check).
• If you issue a refund outside of your QuickBooks Payments. If this happens, send proof of that payment to us.

You are given an option to respond if an amount is disputed. To learn how, please see this article: Handle Chargebacks and Retrieval Requests for QuickBooks Payments. Then, go to Step 2: How to respond and select Respond to a Chargeback. I also suggest browsing up to Step 4 to ensure everything is handled properly.

To avoid this in the future, I encourage checking out this article for the detailed steps: Prevent Future Chargebacks.

I'm only a post away if you need more help in managing the disputed amount.  It's always my pleasure to help you out again.

Quickbooks is sorely mismanaged by morons. They are not protecting small businesses. They awarded charges to the customer on rendered services with signed authorization they agreed to pay yet cited that there was no authorization. They outsource their work to a bunch of morons. 

The total invoice for the customer is $2,526.20. Since the job was completed in full, Customer chose to split the payment—$1,200 via e-transfer and $1,326.20 by credit card, which he has now disputed.
It is not fair to the service provider to dispute payment after services have been rendered in good faith and as agreed.