This feature is currently undocumented.
NNTP
On the Advanced Settings Tab of the NNTP Internet Account document there is a field entitled, "Use Replication history when replicating." Setting this to "Yes" allows the replicator to start pulling articles based on where it left off on the previous replication. This is the default setting and this is the most efficient way to replicate NNTP databases. Setting this value to "No" will force the replication to check every article (starting with the first one) and determine if it needs to be pulled into the replica. You should set this value to "No" if you delete articles from your replica and want to get them back.
IMAP
On the Advanced Settings Tab of the IMAP Internet Account Document, there is a field entitled "Use Replication history when replicating." Setting this to "Yes" allows the replicator to start pulling messages based on where it left off on the previous replication. (Note that messages that are modified, deleted, moved, or copied in either the replica or the server mail file will still be replicated.) Setting this option to "Yes" increases performance with negligible side effects, so most users will want to leave this option set to "Yes".
If you set "Use Replication History" to "No", IMAP replication will check every message (starting with the first one) and determine if it needs to be pulled into the replica. You may want to set the option to "No" when using the Universal Inbox in order to re-pull messages that you have deleted from the Universal Inbox. Note, however, that if your Universal Inbox is a server-based mail file, you will receive duplicate messages if you set this option to "No."