It is not possible matching multiple downloaded transactions to a single transaction in QuickBooks. As a workaround, you can exclude the transactions from the banking section, and then clear the one recorded in QuickBooks Online.
To exclude the transactions:
On the left Dashboard, click Banking.
Find the transactions and check the boxes.
Click the Batch Actions drop-down list.
Choose Exclude Selected.
To clear the transactions from the bank register:
On the left Dashboard, click Accounting and click Chart of Accounts.
Click the View Register link under the Action column of the bank account where the transaction is posted.
Click the Funnel icon above the Date column to find the transaction.
If you find the transaction, click on it to expand and place a letter C under Reconcile and Banking Status column.