Can you run Retrospect from a third partition? Neither the one your copying "from"~nor~ the one your "copying too"?
If you haven't physically removed or altered the preferences in the FROM disk, all should be as it was. Only the copy will have lost files.
If you can.....install Retrospect on a third disk (partition) and duplicate to> the copy disk, if no disk is available,
reduplicate the "FROM" disk, it should fill in the blanks. (and be a very small file duplication) I've had the experience (in OS8.6) that retrospect will get caught on something and stop in it's tracks. I would close out the application and reduplicate, somehow it's would find a way to overcome the problem.
Also, if there is not enough Memory allocated to the application, or if you use Virtual Memory and you have no space, this can stop retrospect.