I’m having the same issue. Never experienced this prior to 5.6. Incredibly frustrating, surprised no one else raised this problem sooner.
Issue seems to affect all imported assets that are not actively loaded.
For example, if I create a folder under Content called ‘Meshes’ and import an .fbx file, then close and re-open Unreal Editor, I can no longer see the Meshes folder in the Content Browser. If I manually browse to that location with Windows Explorer I can still see the Meshes folder in MyProject\Content\Meshes and the .uasset file in it. No folders or assets have been deleted, the Content Browser is just failing to show it for whatever reason.
Workaround: Drag and drop the fbx somewhere into the current default map so it loads at launch.
Additional:
If I click on the Gear icon on the right hand side of Content Browser, ‘All Folder’ is already ticked.
If I right-click on the Content folder and select ‘Validate Assets in Folder’ I see no error messages and the issue persists.
If I right-click on the Content folder and select ‘Update Redirector Referrences’ I see no error messages and the issue persists.