This points to transactions still marked reconciled (R) even after the formal reconciliations were undone. One of the standard causes of a wrong beginning balance is that a transaction dated before your last reconciliation's ending date was reconciled manually, thus adding it to your beginning balance outside of a reconciliation.
Undoing an entire reconciliation only reverses the transactions tied to that specific completed reconciliation report; it doesn't undo transactions that were reconciled manually in the register, separately from a normal reconcile session. If an earlier reconciliation was done by checking things off directly in the register rather than through the guided Reconcile flow, undoing the formal sessions afterward won't clear those manual R flags, and the beginning balance will stay off by exactly that amount. Since nothing about those transactions' amounts changed, the Discrepancy Report has nothing to flag either, which is why it comes back clean.
How to find and clear the leftover reconciled transactions:
- Go to All apps, then Accounting, then Chart of accounts, then select View register for the account.
- Filter the register by Reconcile status and look for any transaction marked R dated after your last completed, correct reconciliation.
- Open each one you find and select the R box repeatedly until it's blank, then save. This unreconciles it without deleting it.
- Once the stray R transactions are cleared, go back to Reconcile: the beginning balance should now match your last good reconciliation and your bank statement.
Two things worth checking alongside this:
- If the amount you're off by doesn't fully clear after this, also check the Audit Log (Settings, then Audit log) for the same date range, since deleted or voided transactions from that period won't show on the Discrepancy Report either.
- Do this one period at a time, oldest first, the same way you were already working backward, so you can confirm each beginning balance matches before moving to the next.
For the full current steps and the complete list of causes: Fix beginning balance issues when reconciling in QuickBooks Online. For what Undo does and doesn't cover: Undo or remove transactions from reconciliations in QuickBooks Online.
Given how many months you're working through and that this touches prior-period equity, it's worth having an accountant or bookkeeper glance over the corrected balances once you're caught up, just as a second set of eyes rather than because anything here suggests you've done this wrong.
