I don’t think it was the degradation—it failed again this morning. But—after unchecking the “Force overwrite already migrated articles” checkbox, everything migrated OK. There are likely minor variations somewhere between the new articles, revised articles and untouched content that got things confused. Everything worked in the end though.
Wouldn’t have to do this dance except I still have HTMLResources.zip at play in this book.
I came across the same issue with another customer a few weeks ago, it turned out it was project specific. What we did at the time is we made a slight change to the project name (just added a number at the end) and then reverted back to the original name. After that it looks like it fixed the project itself and we were then able to migrate the Folio that originally failed.