I am getting duplicate transactions based on configured rules, at least it appears to be the cause. How do I track this down and also how do I easily reconcile thousands of duplicates?

Hello there, djbelcher.

You can filter the transactions list by the type of bank and the date range. It'll be easier for you to identify the duplicates and you can select and exclude them by batch. 

Let me show you how:

1. Go to the Transactions menu.
2. From the Type drop-down, select the type of transaction and the bank. 
3. Under Date, you can customize the date to display.
4. Once the list refreshes, you can select the duplicates and then click the Exclude icon.
5. Click Apply.

To help you manage bank downloaded transactions, you can check out these resources:

• Categorize transactions in QuickBooks Self-Employed
• Create rules to speed up reviews in QuickBooks Self-Employed

Keep me posted if you have other questions. Take care!