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.