Final answer:
In response to missing controls in the accounting system, an auditor would modify the audit program to increase substantive testing and possibly suggest control improvements.
Step-by-step explanation:
When the auditor finds that there are missing controls in an area of the accounting system, the audit program in that area would be modified in such a way as to increase the level of substantive testing. This means that the auditor will perform more detailed checks on transactions and balances to ensure the reliability of the accounting records because the lack of control increases the risk of errors or fraud. The auditor may also suggest improvements to the internal controls system and verify their implementation in the future.