Had a long talk with Apple Support today. I made it clear that I'd tried the obvious things (like running Disc Utility) and was more interested in reporting the issue to the highest level, rather than being talked through basic steps.
They actually responded to that very well, and it was largely an information-gathering exercise. They said they'd had other reports like this. By the end of the call I was with a second-tier operator who really dug down and took lots of info, so I am pretty encouraged they really do want to get to the bottom of this. It's all been passed on to their "engineers". I'm expecting a call-back on Thursday. Overall, I'm pleased to have been very impressed with their response thus far.
The first operator did suggest one fascinating nugget of information -- that he had heard that some drives to which this kind of thing has happened have been left connected for a while, and the files have "reappeared"! Perhaps somebody would like to try for this on one of the test discs that have been mentioned. Meanwhile, Apple unsurprisingly agreed that it was probably wiser to leave my drive disconnected pending the results of the investigation.
Finally, since someone has asked for this, in my case it's an early 2009 MacBook, 5.1, that's involved.