Hi there, @amnevarez.

Allow me to dive into this thread to assist you. I'll explain your concern about the affected invoice in the payment transaction. When you click edit and delete a transaction, you'll get an error message: "You need to delete this payment from the deposit before you can delete the transaction itself." 

When you delete a payment from a deposit, you need to remove it from the Deposit first before deleting the individual payment. This is a security measure to prevent accidental or incorrect deletion of transactions.

So, the first thing you need to do is to open the invoice:

1. Then click Deposit.
2. In the deposit window in the amount column, you need to zero out the amount.
3. Then Save and Close.

Here is a photo for your reference:

In case you need to fix payments that have been deposited or reconciled already without affecting your reconciliation, check out this article: Correct customer payments that have been deposited or reconciled.

Feel free to reach out if you need help with your invoices or anything else. I'm always happy to assist in any way I can. Have a great day!