When inactivating a task within MS Project, remove the predecessors and successors first. Check the logic of the related tasks to make sure they are properly linked to new/different tasks. Then inactivate the task.

Process Improvement
The ISO 9001 Audit Mistake Most Companies Make Before the Auditor Even Arrives
If you’re preparing for an ISO 9001:2015 audit, one of the biggest mistakes you can make is treating audit readiness like a last-minute checklist instead