If you want to use both User and Project pages on GitHub Pages, then you need to create the User page first. Project pages created before the User page will no longer be accessible. To restore the project page, make any change to the gh-pages branch for the Project page, commit and push.

I’m guessing this is related to the name structure used. Project pages are http://username.github.io/repository and User pages are http://username.github.io, so Project pages are in a broad sense “subdirectories” of the User pages. Initializing the User page thus blocks the existing subdirectories, in case you have a subdirectory in the User repository with that same name. Changing the Project gh-pages branch re-initializes / refreshes the Project page, restoring the mount point.

What happens when you have a name collision?