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Correct. Duplication is inheritted unless explicity set. Enabling pool file duplication enables it for the root, and everything else gets inherrited. And when you change it, it checks to see which files need to be duplicated or unduplicated (the "checking duplication" part that you may have seen). So, it shouldn't mess with the existing data.

First, I'm sorry to hear about your drive, as that is never a pleasant experience. You may be able to use "dpcmd ignore-poolpart" to eject the drive from the pool. This marks the drive as removed, but doesn't move any of the files off of it, and causes the drive to show up as "missing" in the UI. This does require writing to the drive, to write the tag that marks it as removed. Once the drive is ejected, you can manually move the files over. The poolID for the drive is the name of the hidden "PoolPart.xxxx" folder on the disk (with or without the PoolPart part).