How does an IBM Domino server determine which documents to replicate for an application? 

Only those documents marked for replication by the user are replicated. 

The Domino server checks each document for the "$Has_Replicated" field. 

The Domino server checks replication history and replicates only those documents that have changed since the last replication. 

The LastUpdated property of the application is checked. The Domino server replicates only those documents added since the LastUpdated time.