I wrote about a couple of times in different places; if you have an URL like notes://Domino1/replicaID/0/UNID?OpenDocument, but you last worked with a replica on server Domino2, the document will be opened on Domino2 and NOT on Domino1 as it is given in the URL.
In fact, the server where Notes opens the document depends on the chicklet of the appliation in the workspace. Notes will always use the server that is "active" for the application's chicklet in the workspace.

That. Is. A. Pain.

I stumble across this issue over and over again, here at YouAtNotes and at customer applications.

So, please, dear developers at IBM, we talked about that in the design partner forum some months ago, please please please fix this.