Fixed all the warnings and the issue still persists.
Only exception being this which shouldn’t be an issue as far as I understand.
UATHelper: Packaging (Windows (64-bit)): Cook: LogInit:Display: LogModuleManager:Warning: ModuleManager: Unable to load module ‘OnlineSubsystemSteam’ because the file ‘E:/Unreal/UE_4.16/Engine/Binaries/Win64/’ was not found.