Delete a check that was reconciled, but never deposited?

Hello there, VMRInc. 

When your bank account has non-sufficient funds (NSF) or doesn’t have enough money to cover the check amount, your bank charges you an NSF or bank fee. 

You can check out this article for more tips on handling bounced checks due to NSF in QuickBooks Online: How to record customer's bounced checks using Accounts Receivable.

To delete the payment, you can unreconcile the entry first.

Here's how:

1. Go to the Gear icon, then select Chart of Accounts.
2. Select your account, then tap on View Register under Action.
3. Locate the transaction, then remove R from the checkmark column.
4. Choose Edit, then Delete.

However, I'd suggest consulting an accountant before performing the process to avoid discrepancies in your records and previous reconciliation.

Additionally, I've added this article in case you encounter errors while reconciling: Fix issues for accounts you've reconciled in the past in QuickBooks Online. 

Let me know if you need further assistance with your reconciliations. We're always here 24/7. Stay safe.

@VMRInc 

"The payment was input as an NSF and reconciled way back when, but it appears to have never been properly deposited."

Your question is a bit confusing because, if the payment received is still showing on your bank deposits page, then it hasn't been reconciled.  You can't reconcile a payment received until it is deposited.  Are you on cash or accrual basis?  Did the customer eventually pay the invoice?  If so, how was that recorded?  The issue here is that you need to reverse the deposit entry with a check or expense entry and then clear them against each other.  If this payment is still sitting incorrectly in undeposited funds, then there is another account that is overstated by the same amount.  The question is what account to assign to the check or expense entry to correct that side of the transaction.  That depends on your answers to the questions above.