I know this probably isn’t very helpful, but check your project NMake paths. You might be pointing to the default engine install from the launcher rather than your github checkout of the actual source.
All I can recommend is that you check out the github repo, redo your changes there and have another go at building it. This is the method we’re all familiar with.
You can not rebuild the launcher version, you need a source build which you get from GitHub. The launcher build comes with the source just for debugging purpose.