Of course, my manual copying of the offending folder and the subsequent smart update didn't work.
So thank you for the quick answer. I unlocked the original folder, did a new Time Machine backup, and went through the other 30-something Time Machine backups to check the folder was unlocked everywhere. I had to unlock it manually twice, I think. Probably where the folder had actually changed and was not just a hard link.
I'm starting a new SuperDuper "erase, then copy" action. I'll feel better if it works at once, rather than after my smart updates and my tinkering. I'll write back in a day or two to report how the cloning went.
Thanks!
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