It's ease to keep it up to date. I added my scss files to bootstrap.scss, so if new version of bootstrap will be released all I need to do is update bootstrap scss file in my project.
Are you instead just going into bootstrap.scss and commenting out entire includes?
The former implies a lot of surgery and the latter is definitely more manageable, but could still suffer from the project abandonment he brought up.
All in all I liked what I saw :)