This happens when the last reconciliation was changed or deleted by other users that's why it is showing as unreconciled. You'll want to check the Audit Trail to verify if there are changes made in QuickBooks.
- Click Reports on the upper menu.
- Select Accountant & Taxes.
- Choose Audit Trail.
Once done, you can do a mini reconciliation to make the correction.
However, for those transactions that are still showing as reconciled, you can run the Reconciliation report to fix the issue: Fix Issues When You're Reconciling in QuickBooks Desktop.
You can get back to me to this thread if you need further assistance in QuickBooks. I'd be glad to help.