Thanks for the feedback everyone.
I tried Todd's suggestion of minor changes to the guilty methods, but didn't see any change to the status of the classes - I suspect that the references may be too obscured for me to uncover them all.
Running Bert's fix removed the immediate issue, but then RB had a problem with anObsoleteT1 (Trait) created by the same suite of tests. This appears to be totally unreferenced and I don't understand Traits at all so I'm ignoring it, as I've come up with a fix for RB.
So as Jerome suggested I've raised the bug on Mantis (#5910).
I've added a simple fix to RB as bug #5911 which makes it exclude obsolete classes from its consideration. This allows RB to refactor successfully, but I can't guarantee that it doesn't introduce any issues.
Cheers, Michael