Yes, it’s possible to backup only select repositories.
BackHub creates backups of all repositories it gets access to by default. If you want to backup only select repositories you can simply limit access to those repositories.
In the installation dialog, you choose whether to give access to all or to only select repositories. Choose “select repositories” and type in the names of the repositories to backup.
If you have already installed BackHub, you can edit the permissions by managing your installations on GitHub.