See http://blog.sonatype.com/people/2012/02/nexus-pro-2-0-support-distributed-teams-with-smart-proxy for an introduction to Smart Proxy.
Nexus Smart Proxy feature is not a replication technology, and was not designed to keep both sides perfectly in synchronization in terms of what is in their local storage. It's aim is to make sure that your builds never break because cache timeouts are blocking the download of something. Nexus Smart Proxy Preemptive fetch will only retrieve newly deployed artifacts.
There are circumstances where the number of potentially changed artifacts is so large that we don't send fetch events for individual artifacts. In this case the remote is told to clear it's entire not found cache. Since the proxy caches will be cleared, if someone requests them through the remote instance they will be downloaded and served.
Other cases which are not helped by Smart Proxy are centered around proxies of group repositories. For example:
- Routing rules for the group are changed, making new artifacts accessible
- Repositories are added/removed from a group, exposing or hiding artifacts
There isn't a way to synchronize these changes.
Again, the focus of smart proxy is not replication, it is cache management.