This just happened with our studio.
Multiple objects were all separated on layers that are not seen in layerview, yet are in hierarchy view. I had to reopen the file to update a rig and do a save/load, and there was no way to easily access the controllers, save to expand all and wait.
Once I merged the new rig in, the layers for it appeared from the merged file, but only those layers.
Unfortunately the 2014 trick cant work for me because we have stuff xrefed in, which cannot be opened in 2014 because they are 2016 files. We could see the layers for non xrefs, but it nuked all the xrefs.
It seems to be saved right at the node level because merging the file into a clean working one doesn't work.
I'm not sure if this is related, but in this corrupted file, the nodes in the scene are not reacting to the hide by category in the display panel in the viewport. They are rendering according to the panel settings, but when hiding bones and shaped they still appear in the viewport, yet are not selectable and are not renderable. They do react correctly in a previous iteration that has a working layer viewer.
If anyone has found a fix, or took the time to write a script that reads and creates new layers from the nodes in the scene, that would be awesome.
Josh