Hey -
Sorry for the delayed response. I was able to reproduce this issue by attempting to build a project with the Build/ folder missing and have submitted a bug report (UE-12556) for further investigation. For the time being it should be possible to build the project if the Build folder is included when checking in/out files to perforce as NisshokuZK mentioned in the forum thread. Additionally you can copy the Build folder from another local project after check out which should allow the build process to complete as well.
Cheers