No guarantees here but off the top of my head I'd go about it like this using a few custom buttons and DOpus flat view.
Set up a dual lister with your source in one pane and the target in the other. Next one at a time, put both source and target in FLAT mode with this command:
Then select all the files in the source pane and run the following command to select the same files in the target pane.
Next make the target pane active and invert the selection so only non matching target files are selected with this command:
And finally run this command on the target pane to hide everything that has a match in your original source pane.
Select HIDEUNSEL NOPATTERN
Which should leave only the orphans visible in the target pane.
I haven't extensively tested this, but it does appear to work even when the file paths to the files are not identical. It does not seem to work on hidden/system files however but it might give you a start.