Can you assign a reconciled deposit to an unpaid invoice ?

Any changes made to your reconciled transaction such as editing or deleting may affect your books. You'll want to make the changes directly from those transactions that were already reconciled. 

You can temporarily undo the reconciliation then edit it to link it to the invoice. After that, you can manually mark it as reconciled to the bank register.

Here's how:

1. Go to the Banking menu at the top, then pick Reconcile. 
2. In the Begin Reconciliation window, select the appropriate account, then click Undo Last Reconciliation.
3. Tap Continue, then OK. 

You can then make the necessary changes to the bank register as necessary. Then proceed with reconciliation once you're done. 

To mark them as cleared, you need to each transaction or the transactions you want to reconcile manually from the Reconciliation window.

Here's how:

1. Go to the Banking page, then click on Reconcile.

2. Fill in the information under the Begin Reconciliation window.

3. Tap on Continue.

4. You can click on the Mark All button to mark all of the transactions from the list. Or, manually mark the transactions you want to reconcile.

5. Once ready, hit on the Reconcile Now tab.

In case you run into issues or discrepancies, here's how to fix mismatches and other reconciliation issues:

• Fix Beginning Balance issues in QuickBooks Desktop
• Fix issues while reconciling accounts in QuickBooks Desktop

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