Something similar happened to me with 4.16.1
Without changing anything related to the Blueprint in question, one of three pretty much equivalent child Blueprints lost its skeletal mesh reference every time I restarted the editor. The sibling Blueprints were fine.
The hierarchy was C++Class->BlueprintClass->BlueprintClass.
The reference viewer revealed that a Redirector had a reference to the Blueprint. Weirdly, even after deleting and recreating the Blueprint, the problem persisted until I deleted the Redirector.
After deleting the Redirector and the Blueprint and then recreating the Blueprint, the bug no longer occurred.
Maybe this is helpful.