When a secondary node is replicated to the client, the method _OnReplicationNodeAdded will be called on the primary node in the replication group. If you want to keep references to these objects on the client, you'll want to respond to that event by storing their IDs or noderefs in whatever manner you deem appropriate (e.g. associations, list of noderef, fields, etc).
So, for example:
method _OnReplicationNodeAdded(addedNode as NodeRef)
where addedNode is kindof NodeClassICareAbout
AddAssociation(me, "MyGameSpecificSoftAssociation", addedNode)
.
.