Having the wrong server address in the “Ports/Notes Network Ports” tab of the server document causes the message “ has not been opened yet” on web/server side agents.
I figured this because, after moving my application to a new server, the call to the method “NotesDatabase.openByReplicaID(serverName, replicaID)” started to fail.
My code uses the property “NotesSession.CurrentDatabase.server” to get the serverName parameter, so this datum could not be wrong.
But reading through this forum I saw a couple of posts where their authors claimed that either leaving the server name blank or using its IP address helped to avoid the message.
So I checked out the server address and found that, by mistake , a zero was occupying the space of an “O”. (duh 
I saw several posts related to this problem. Hope you find this useful!!