I have been working with a huge map document with thousands of layers, and encountered this weird error where by if I tried to zoom out, one of the layers disappeared. If I zoomed in, it appeared again.

I have tried many solutions I could google out for a few days, but nothing worked. I put my problem on geonet.esri.com discussion board and waited for the help. To my surprise, one user responded my question with a few precise suggestions and my problem has solved. The solution which worked for me is simply to copy the feature layers over to new map session.

Following is the link to the thread on geonet.esri.com where I got the help. 🙂
https://geonet.esri.com/message/451155#451155