I’m glad you figured it out! 
I’m assuming this happened while upgrading to 5.6. If you’re planning to do so again, I’d maybe recommend starting with a clean 5.6 project, exporting all of your current 5.5 stuff through the Export tool in UE, and then Import it into the new project, just in case.
Also, definitely look up version control software so you avoid these kinds of issues in the future. xD