I collect early 20th century boys' series (Tom Swift, etc.) and this can be a really annoying issue. Of course, the annoyance starts with the book packagers, who decided they'd take books 1, 2, and 3 of an existing series and make them books 5, 6, and 7 of another series, or re-issue an existing series with some of the books rearranged, apparently just to make collectors who hadn't even been born yet tear our hair out in bloody chunks.
Mostly, I've just given up. But to the extent it can be fixed, I think it's going to have to be done manually, as people suggested above. (and in my case, a time machine and a list of people to yell at might help)
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