Steps to reproduce:
1. open User's project and upload it to the Collab server
2. open Internet Browser and go to https://developer.cloud.unity3d.com/projects, select the project
3. Overview Tab > Go to Collaborate > Assets (tab) > Assets (folder) > test2 (folder). Notice: NavMesh file is here
4. switch back to Unity
5. Assets > test2 (folder) > NavMesh
6. bake again: Window > Navigation > Bake (button)
7. upload changes to the server
8. switch back to Browser and refresh the page

Result: NavMesh file is gone from the server

Reproduced with: 5.5.0b3, 5.4.1f1
Not reproduced with: 5.3.6p4 (there is no Collab)

Note:
-when deleting the project from computer and re-downloading it from the server NavMesh file does not appear