I used the same service (I believe) through the local Ferragamo store, as detailed here:
http://www.styleforum.net/t/268411/ferrogamo-tramezza-restoration-service/0_40#post_4859111
Anyhow, I got them back today. Interestingly my shoes are the same as Storm33's, but in 13D size. The service was a "full restoration" for $140. The entire outsole was replaced, including the instep area with the logo... there's no size or Ferragamo "logo" or branding on the new sole. Yet strangely, there's a faint "Made in Italy" on the new heel. Both the front and rear have new rubber as well, although the configuration is different than before.
The inner sole was also replaced and again, the replacement has no branding. This has the effect of removing all traces of Ferragamo branding from the shoe. The quality of the new innersole seems very good, and the uppers definitely seem to be in better condition than before.
All in all, replacing the entire sole and heel with high quality parts, including the inner sole, plus reconditioning the uppers, new laces, sent back with a new box and bags, for $140 seems like a reasonable deal. My local cobbler wanted $90 for just the sole and couldn't guarantee he could replicate the leather/rubber hybrids that these shoes use.