I opened a PMR with IBM. Answer is that this is 'working as designed' and has been that way for ever it seems and IBM just haven't bothered to fix it. And they wonder why Notes loses market share year after year.

Anyway, we are looking at the possibility of using an agent to update the roaming replica field in the person doc and manually replicating the files.

Only other workaround is to un-roam and then re-roam the users. Not a great option as the un-roam has to complete before the re-roam or game over.

IBM Response: If my understanding is correct, I've checked for this situation in our knowledge bases and it appears to be "working as designed" at present.
I can see two Enhancement SPRs the latest of which is YHNN8EQNRC R9.0 (Roaming: Support for move user's roaming files for clustered Roaming servers) which outlines the following..

In Lotus Domino Administrator, one can only move the roaming user files for the roaming server, the Roaming Replica server is ignored.
As a result, only the files from the roaming server are moved to the new server and only the roaming server is updated in the person document.
To move the roaming replica server files, additional (manual) steps have to be taken:
1. Replicas must be move from the old roaming replica server to the new roaming replica server
2. The roaming Replica server must be updated manually, which is not supported AFAIK

Similarly in the other SPR WSZO7JSUXL R8.0 the information for the customer report goes as:

Problem: You want to move the roaming User from a Domino 6.5.6 Mail Cluster to an ND 8.0 Mail Server via AdminP >Move User. When you move the user, you find that the mail file is moved to 2 servers at a time, however the set of roaming files are moved to one server only. You want to overcome it and want the mail files & set of roaming files to both servers at the same time.

To workaround the issue with the roaming replica server not being updated in the Domino Directory our developers have written us some code.

If you'd like the code to use at your own risk, post up here. 

Hello Stuart,

I have the same issue, I'll be interested by the code.

Thank you