The first step the project manager should take is to assess the repository to check for inconsistencies. This is because the stakeholder's concern is about the benefits management plan in the project document repository.
Before making any changes or updates, it's important to first understand the current state of the repository and identify any inconsistencies or issues. This will provide a clear picture of what needs to be updated or changed, and will help ensure that the benefits management plan accurately reflects the current state and goals of the project. References: PMBOK Guide - Sixth Edition, Section 4.4.3.1: Project Documents Updates