[/Script/Engine.RendererSettings]
r.Nanite.CoarseMeshStreaming=True
r.Nanite.ProxyRenderMode=2
[SystemSettings]
r.Shadow.Virtual.NonNanite.IncludeInCoarsePages=0
; Imposters are not necessary because of HLOD
r.Nanite.Streaming.Imposters=0
; Set initial size to we prevent a resize to 6144 at the transition to chase
r.Nanite.Streaming.NumInitialRootPages=5120
; Increase the number of Nanite nodes to prevent some visual issues.
r.Nanite.MaxNodes=2621440
[/quote]
I think the Nanite has some issue. it was not solved.
Hi, July014. your script didn’t work. In fact none of the given solution solved my issue. 
I copied the settings scrips into the DefaultEngine.ini
here is the .ini look of the script
I tried changing the Collision box scale
I tried to change the Bounds extension. Increased it from 0 to 1000000

and
I also tried changing “LOD Settings” LOD Group to “LevelArchitecture”,
!!! None of them work. !!!
In my case I am using a speed tree asset as foliage.
I tried to import the tree in to the scene both as foliage and as simple static mesh in to the level. But it does not work.
If I go far away from the tree it starts to disappear the leaves and at some longest distance I start to lose the tree branches.
here is the screen shot.
If some one found any real solution please let us have it.
And @July014 I think it is not related to the DefaultEngine settings of the project. because I literally imported my tree into the Matrix city sample you are talking about. and it still have the same issue.
close distance screen shot
medium distance screen shot
far distance screen shot