Well, I got there in the end. Windows kept failing to copy the .rockbox folder as it couldn't find various files so in the end I deleted it - I was resigned to revert to the OF if necessary.
Having deleted it chkdsk found no errors with the /f parameter but continued to abort with an unexpected error if I used the /r param. Nevertheless I went ahead with the install and it worked fine. I'm now happily running 3.9.
Thanks for your help