If the replicator software is also copying the metadata.db file then you should see the new books.
Issues that might cause this not to work are:
- calibre being open on the source computer and locking the metadata.db file so it cannot be replicated.
- calibre being open on the target computer so the metadata.db file cannot be written. Even if it was, calibre expects to have exclusive access to the metadata.db file while it is running so would not see any changes.
In short, as long as you replicate both the book files and metadata.db file, and Calibre is not running at either end while this takes place then it should dock OK.