When opening a map with ISM in place, NavOctree is not updated because the ISM bounds are assumed invalid and the geometry is not taken into account in the navmesh build. The following log output is generated at this time.
LogNavigation: Warning: FNavigationOctree::AddNode: Empty bounds, ignoring InstancedStaticMeshComponent /Game/Developers/Collections/ism_cs_nav_test.ism_cs_nav_test:PersistentLevel.BP_ISM_C_1.NODE_AddInstancedStaticMeshComponent-0. LogNavigation: Warning: FNavigationOctree::AddNode: Empty bounds, ignoring InstancedStaticMeshComponent /Game/Developers/Collections/ism_cs_nav_test.ism_cs_nav_test:PersistentLevel.BP_ISM_C_1.NODE_AddInstancedStaticMeshComponent-0.
Manually changing the ISM location or updating the bounces will eliminate this problem. Also, if this map is set as the startup map when the editor is launched, the problem does not occur. This is most likely a regression in UE5.5.