Comprehensive and Detailed In-Depth Explanation:A post-implementation review (PIR) of a newly modified IT application focuses on ensuring that the system meets business and security requirements effectively. The sufficiency of implemented controls (A) is the most critical aspect because it ensures that security, operational, and compliance controls are functioning correctly. These controls include access controls, data integrity checks, and audit logs to prevent unauthorized access, data corruption, or security breaches.
Other options:
* Resource management plan (B) is important for project management but is not the primary concern for an IS auditor in a post-implementation review.
* Updates required for end-user manuals (C) are necessary for usability but do not impact the security or operational integrity of the system.
* Rollback plans for changes (D) are important for change management but are typically assessed before deployment, not in a PIR.
Reference: ISACA CISA Review Manual, IT Governance and Management of IT

The auditor should first escalate to audit management to discuss the audit plan. This is because the audit plan should be based on a risk assessment and aligned with the organization's objectives and strategies. The auditor should not accept the CIO's request without proper justification and approval from the audit management, who are responsible for ensuring the audit plan's quality and independence. The auditor should also communicate the potential risks and implications of not conducting IS audits in the upcoming year, such as missing new or emerging threats, vulnerabilities, or compliance issues. References:
* CISA Review Manual (Digital Version), Chapter 2, Section 2.11
* CISA Online Review Course, Domain 1, Module 1, Lesson 22

The use of control totals satisfies the control objective of processing integrity. Processing integrity refers to the accuracy, completeness, timeliness, and validity of data processing. Control totals are a method of verifying the correctness of data processing by comparing the total value or count of a batch of transactions before and after processing. For example, if a batch of 100 invoices is entered into an accounting system, the total amount and number of invoices should match before and after processing. If there is a discrepancy, it indicates an error in data entry, transmission, or processing. Control totals help to ensure that no transactions are lost, duplicated, or altered during processing.
References:
* Control Objectives & Activities: Examples, Appropriateness
* Levels and Types of Control | Principles ofManagement
* CISA Review Manual 27th Edition, page 337

If an IS auditor suspects that independence may not have been maintained in past audits, the best course of action is to inform audit management. Audit management has the responsibility and authority to address such issues. They can review the situation, determine if there was indeed a lack of independence, and decide on the appropriate actions to take123. While informing senior management, reevaluating internal controls, and re- performing past audits might be necessary at some point, the first step should be to inform audit management.