We recently just brought our ArcGIS Server 10.3.1 site down from 2 Servers / 2 Web Adaptors to 1 Server and 1 Web Adaptor. I published a map service today and noticed the layers were not populating in the rest end point. The layers do not work in a web application either. Anyone ever experienced this? I'm inclined to think this is going to require a fresh install to fix it. See hte 'Layers:' below in the screenshot. A list of the layers in the map service should be there but they aren't.
I've already restarted ArcGIS Server service. I will reboot the machine tonight to see if that fixes it.