Hello as the title said, we are currently facing the same issue as described by this bug UE-243852 where some layers will not load properly, but we are using a fully dynamic navmesh inside our world. Was the bug tested with a full dynamic navmesh aswell? We are currently on 5.5, but cannot test fully yet on 5.6 and up, but we did import the fix as a cherry pick.
Link for reference Unreal Engine Issues and Bug Tracker (UE-243852)