I had this issue; my build although was pointing to a source version of the engine, it somehow was linking to the Epic Launcher version of the engine when building for some parts.
For my instance, it was due to having the project living on a networked isilon drive. I had to delete my Epic Launcher version of the engine and rebuild the source and clear out the solution file of the project and rebuild that. Once all that was complete the EOS target built fine for me.