I had a couple of referenced objects and, on one, I deleted a bunch of constraints after baking keys for joints & controls in both referenced objects.
I'm thinking that the reference edits just piled up and Maya needed to do something with them before moving on when trying to create a new file or load another. In this case, saving the file was enough and, by far, the fastest way to deal with the problem.
Everything was performed in Maya 2017r5. Since everything I'm working on is proprietary, I don't have anything to share, unfortunately.