If I click yes to rebuild the .dll it will fail. If I open the .sln file and rebuild solution after cleaning the binaries the .dll file reappears in the binaries folder but if I try to open the .uproject again I get the same message.
The following modules are missing or built with a different engine version: UE4Editor-[GameName].dll
We experienced this issue when our *.modules files weren’t commited to source control. Are these missing for you?