Can't import repositories using gitlab-rake gitlab:import:repos

After a gitlab upgrade (from 7.9 to lastest with omnibus package), I have lost all configuration, and found that the backup I made was empty, so I could not restore a backup.

I've found that I still have the old repositories in /home/git/repositories/ so I've copied them to /var/opt/gitlab/git-data/repositories and changed the user recursively to the gitlab user.

Now I have used the command gitlab-rake gitlab:import:repos and it has processed all repositories and has created the groups with an output like this:

Processing fib/sdx.git
 * Created sdx (fib/sdx.git)
Processing fib/sdx.wiki.git
 * Skipping wiki repo

The problem is that although it has created all groups and now I can see them in the gitlab web interface, it shows that each group has zero projects

¿How can I recover these reposistories?