Bank Reconciliation

I recently took over the bookkeeping for a company effective October 1, 2026. The bank account had previously been reconciled through June 30, 2026.

When I went back to complete the July reconciliation, QuickBooks showed that the beginning balance was off by approximately $48,000.

I contacted the CPA firm that reviewed the previous bookkeeper's work. They explained that during their review of January through June 2026, they found that the prior bookkeeper had double-booked certain payroll transactions. Those duplicate transactions had already been included in completed bank reconciliations, so the CPA firm deleted them as part of cleaning up the books.

It appears that deleting those previously reconciled transactions is what caused QuickBooks to now show the $48K beginning balance discrepancy.

The important part is that the current book balance agrees with the bank statement. I went ahead and reconciled July, and at the end of July I am still off by the exact same approximately $48K beginning balance difference.

What is the proper way to clear/fix this historical beginning balance discrepancy without changing the correct current book balance?

I don't want to recreate transactions or post an adjustment that would change the general ledger/bank balance just to make the reconciliation screen work. Is there a way to repair the reconciliation history or otherwise clear the discrepancy caused by deleting previously reconciled duplicate transactions?

I'm using QuickBooks Online.