Hi there, @Jim293.
I appreciate you for trying the basic troubleshooting steps before reaching out to us here in the Community. Glad to know that you're able to resolve the error you've encountered while trying the Verify Rebuild tool.
Since the old transaction still shows in the Payments for Deposit registry even after trying the verify rebuild, I'd recommend you contact our Customer Care team. They can pull up your information and review your transactions to help you identify what's causing this to happen. They can also perform an escalation whenever needed to investigate the issue.
I'm adding a help article for your future reference, read through: Correct customer payments that have been deposited or reconciled. It contains different scenarios that can help you adjust your customer payments accordingly.
Should you have more questions, feel free to message again. We're always around here to help.