Hello, ARbooks.

Form your description, you're on the right track in correcting a deleted reconciled transaction in QuickBooks Desktop (QBDT). You'll have to do the same process to your other account, so its discrepancy report will also show a difference of $0.00. I'll elaborate this in detail below.

Once your other account also has a deleted reconciled transaction, re-enter it and manually change its status to "reconciled" to correct its discrepancy. Follow the steps shared by my colleague above to complete the process.

Furthermore, I'd still recommend consulting your accountant to further guide you in keeping your accounts and financial data accurate.

You can learn more about fixing reconciliation discrepancies in QBDT by seeing this article: Fix beginning balance issues in QuickBooks Desktop.

Additionally, I encourage you to reconcile your accounts in QBDT regularly (every month). This helps monitor your income and expense transactions and detect possible errors accordingly. You may want to check out this article as your guide in doing and fixing reconciliations in QBO: Learn the reconcile workflow in QuickBooks.

I'm always ready to back you up if you need more help with bank reconciliation in QBDT. I'll keep the thread open so you can comment back.