The volume does accept the change and if it gets moved the navmesh will rebuild with new area set. The core issue is that setting NavModifierVolume.AreaClass at runtime does not notify navigation system about the change.
1. Open any project and create a trivial map with a platform and navmesh on top of it
2. Make sure navmesh is configured for runtime generation in Project Settings -> Navigation Mesh -> Runtime Generation
3. Put a default NavModifierVolume on the platform, make sure it cuts through the ground.
a. Notice that it does not affect navmesh
4. Add a piece of blueprint that will wait X seconds after Event Begin Play and then will call Set Area Class on said NavModifierVolume and use NavArea_Null as the class.
Navmesh should rebuild resulting in a hole where the volume stands
Head over to the existing Questions & Answers thread and let us know what's up.