Let's get your reconciliation issue sorted out. You may want to check and review the Audit Log then filter the view to Reconciliation to see if an unreconciling process happened. If there are unreconciled transactions, you can manually reconcile them.
Select the Gear icon on the Toolbar.
Under Your Company, select Chart of Accounts.
Locate the appropriate account for the transaction.
From the Action column, select View Register (or Account History).
Identify the transaction to edit.
In the reconcile status column (indicated by a check-mark), repeatedly select the top line of the transaction to change the status of the transaction. Codes indicate the status of the transaction:
C - Cleared
R - Reconciled
Blank - Not cleared or reconciled
You can take a look at these resources to help you reconcile as well as fixing discrepancy issues in QuickBooks Online: