Power Photos app removes duplicates I need to keep when copying photos to a new library
This isn't ideal and I can't guaranteed it working in this case, but this is the roundabout solution that I go for when I want to stop any given OS molesting my files: Zip it. If you put the files that Power Photos is deleting in to a zip, move that zip to the external drive, and then uncompress (unzip), you should end up with the duplicates on the external drive. If you can then copy the unzipped files in to the albums that you want them to be in, your problem should be solved.
Also, are you sure that PowerPhotos is the right tool for this job? I commonly see it deleting duplicates advertised as a feature, rather than as something that you're supposed to avoid.