In QuickBooks Desktop, eliminating or adding a reconciled transaction will affect your beginning balance for the next reconciliation. You can pull up and run any of these reports to locate the difference.
Reconcile Discrepancy report:
Go to the Reports menu, then select Banking, then Reconciliation Discrepancy.
Choose the appropriate Account, then select OK. You now have a list of transactions that were changed since the last reconciliation. Use this report to identify the transaction/s causing the issue.
If you find a discrepancy, note the transaction date and the Entered/Last Modified, which will tell you when the change occurred.
Audit Trail report:
Go to the Reports menu, then select Banking, then Previous Reconciliation.
Select the appropriate account being reconciled.
Select the most recent statement date. Choose Transactions cleared at the time of reconciliation. (Report is displayed as a PDF file) then Display.
Note the statement and the reconciliation creation date.
Go to the Reports menu, then select Accountant & Taxes, then Audit Trail.
Set the Account filter to the account being reconciled.
Select Customize Report.
Go to the Filters tab, then choose Account from the filters.
From the Account drop-down, select the appropriate account.
Go to the Display tab. Set the Date filter with the From field blank and the To date set to the statement date. Select OK.
Set the Entered/Modified filter with the From date set to the previous reconciliation creation date from the PDF, and the To field as today's date.
See if any of the transactions in the report can account for the discrepancy.
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