I think you should only add the text file and the ini entries after having built the engine. Once it’s there, it’s essentially saying “Don’t build the engine, it’s been prebuilt”, which presumably accounts for the GenerateProjectFiles.bat failure.
So this solution is just to mark an engine build as installed/prebuilt. It doesn’t affect the actual process of building the engine or what gets built. If you need control of that, I think you need to look at that new build graph stuff.