@Dazzling_Divine I may have a solution even though It could affect startup time when playing the level depending on how many of the blueprints are in the level. It should be a temporary fix and hopefully Epic can fix it. You should send a bug report to Epic.
I recreated your blueprint from the video (minus setting materials). I used the Shape_Plane mesh from the starter content. I was getting the same issue when reopening the level. The Blueprints were not updating InstancedStaticMesh components on the NavMesh.
The issue seems to be that the InstancedStaticMesh components are loading with empty bounds when the level is opened. I get this navigation warning when opening the level.
So for a test, I moved the code from the Construction Script to an Event named Build.
Added the Build Event to the Construction Script.
Then on BeginPlay I clear the Instances and rebuild them at runtime which seems to also update the NavMesh.
When playing the level if you hit the console key and type show Navigation you can see the NavMesh.
Even though this is not ideal, it should help until Epic can fix it.
I think Epic updated the code for Navigation in 5.5 for NavLinks to be generated and may have caused a few issues. lucky the two bugs I had got fixed in 5.5.4.