If I delete the tools folder… how can I go in and change the filenames? 
So delete the folder, run SetupAndroid.bat, then rename things?
I’ve deleted build-tools, ran SetupAndroid.bat… and build-tools doesn’t show up again.
.bat file is looking for paths in certain places and even some version numbers are incorrect. I wonder where SetupAndroid got its information from?
Yes; my “Users/…/Sdk/ndk” folder is empty.