I need to stop second-guessing myself.
Had an old FAT32 drive that I'd been meaning to back up for years. Finally got around to popping it into my external enclosure today, and decided not to hook it up to my Deneb. Instead, I hooked it up to an XP machine which promptly decided to corrupt the single most important directory on the drive. Brilliant.
So remember kids, if your Amiga can do something, it can do it better than Windows.