ERROR was encountered while scanning document for compatibility issues

Hi, 

I have a document I need to flatten but when I attempt to do so, I receive the above error message.  

This document has been marked up by many individuals so when we go to print, it loses layers... although my layers tab doesn't show multiple layers at all... 

When zoomed out I see everything - when I print or zoom in, I lose content. 

Acrobat Pro DC

Thanks!