Using World Composition, moving the Navmesh and NavmeshBounds from the persistent level to a sub-level results in the size of the navmesh sub-level being roughly twice the size of the decreased size of the persistent level. Running build paths after moving keeps the file sizes roughly the same.
I have been able to get the file size for the sub-level to be what one would expect (navmesh sub-level is slightly larger than the amount the persistent level decreased). To do this, I would:
Expected Result: World_0 has decreased in size and World_0_Navmesh has increased nearly the same amount that World_0 has decreased.
Actual Result: World_0 decreases and World_0_Navmesh increases to be roughly twice the size of the decrease for World_0.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-178234 in the post.