ZagD

I found the reason for this strange behaviour.
I shucked the 2TB Seagate drive that caused the issue and placed it in an external enclosure. It wasn't immediately recognised, because there was some sort of "locking" at the drive's USB controller level, so after removing its controller it would appear as non-initialised in Windows.
I re-connected the shucked drive to its original controller and copied its contents to another drive, then used the clean command in diskpart, re-initialised it, copied back the poolpart folder from the intermediate drive and reconnected it to the pool. Everything went well and the drive was recognised without a glitch.
Now that the drive is in the enclosure and not in its original case with the "locked" controller, Scanner works fine and no more strange disappearing acts occur!
In short... the original drive's USB controller 'dunnit.

Resolving my own issue.
After copying all poolpart folders to an intermediate drive, cleaning the shucked drives & re-initialising them, I copied back their respective poolpart folders and the pool was automatically recognised. It only needed a recalculation of duplication.
So it appears that the poolpart folders contain all information to recreate the pool, regardless of the disk's volume ID. The reason I started this thread was because I saw in a post by Christopher that Drivepool uses the volume ID to identify the disks and I was worried that after cleaning the disks, I wouldn't be able to get Drivepool to recognise them as being part of the pool. Happy ending I guess!
 

They seem to be alright, though I haven't done any formal testing, just eyeballing the speeds given by Windows when doing copies/moves.  I can stream UHDs with no problem.  I've since assembled a system with native USB-C, which seems to've solved the spin-up issue I mentioned earlier.
It's a really nice enclosure that's built like a tank.  If/when I run out of bays, I'll probably get another one.  It's expensive, but only needing the one USB cable (two if you count power) is REALLY nice.  I also haven't seen any temperature issues since converting from the Norco.

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.