Consider that the missing sales orders might have been put on payment hold. Open the sales order and check if a payment hold has been put in the sales order. Override the payment hold or do necessary changes first in the sales order to remove the payment hold.
If the Payment Hold warning is not shown in the sales order, edit the sales order and check if the Payment Method field was set to blank. Below are the steps to edit the sales order:
1. Navigate to Sales Order > Billing/Payment tab.
Note: On View mode, Payment Event Details are not displayed.
2. Click Edit.
3. Navigate to Billing/Payment tab.
Note: On Edit mode, it displays Payment Events details.
3. Add payment method used (e.g. Visa, MasterCard, Amex, etc.), based on the Payment Event Details.
4. Make sure that Get Authorization is not checked.
5. Click Save.
The Override Payment Hold now appears on the sales order, and the sales order should appear in the Manage Payment Holds lists.
*The above steps on checking why a sales order payment hold warning was not shown can be found in another Support Article with the topic "Sales Order on Payment on Hold not listed in Manage Payment Hold, and Override Payment Hold button not displayed in the Sales Order."