I figured out my confusion. Recreating the new entry does not remove the discrepancy from the report. You just need the balance to match again. So if you had more than one issue, like I did, don't try to reconcile again until you've fixed all the issues. I do wish Quickbooks made it easier to see the linked transactions, or tells you that the transaction you are about to delete is reconciled in another account. I'm not an accountant and I can get seriously confused.
