Yes, you’re right. As you can see here
/etc/bumblebee/xorg.conf.nvidia is from the bumblebee package.
you can see how that file is added in the backup array of the pkgbuild.
An array of files that can contain user-made changes and should be preserved during upgrade or removal of a package, primarily intended for configuration files in /etc.
Files in this array should use relative paths without the leading slash (/) (e.g. etc/pacman.conf, instead of /etc/pacman.conf).
When updating, new versions may be saved as file.pacnew to avoid overwriting a file which already exists and was previously modified by the user. Similarly, when the package is removed, user-modified files will be preserved as file.pacsave unless the package was removed with the pacman -Rn command.
See also Pacnew and Pacsave files.
That’s why the package didn’t overwrite your changes. ;)