It's great to have you here in the Community, @k_klink13.
I appreciate you providing on-point details about your situation and a screenshot to get a better picture of your Recon_Invoice deletion.
I'll share some insights about the two payments with the same amounts under your customer file.
It's possible the invoice payment was deposited to Undeposited Funds and the other payment hasn't been deposited to your bank account. This maybe the reason you're seeing two payments for your customer.
Since you've already reviewed on the transaction history and you didn't want to reverse the payment, let's first double check their posting accounts. Here's how:
If it's not yet deposited, you'll need to make sure the Deposit To field for the deposit is selected to your bank account. Here's how:
I'm also including this article for additional insights: Record Merchant Service Deposits.
Let me know how it goes, @k_klink13. Please click the Reply button below if there's anything else I can do for you, I'm always here to help.