Hi @Osiris,
-000x dirs are created not as a backup but as a new cert directory because a new cert with same cn domain (but some domain removed) is already in use. those dirs are also created when you use --duplicate switch or when you add a domain that was not included in the first certificate and don't use --renew-by-default or --expand switches.
I tested it yesterday 7 times (in staging) because of this post 
Cheers,
sahsanu