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In the future (especially if the book is quite complicated/complex), I'd also recommend not leaving validation as the very last step (which I fear we're all probably a liitle guilty of). If you have tons of links, it's probably a good idea to validate regularly--but especially before and after splits/merges or bulk s&r. Things are always easier to fix (roll back) when you know exactly what you were doing when things went pear-shaped.
I know that's not very helpful right now… and I apologize for that, but sometimes there's just no help to be had for "needle in a haystack" type situations like this.
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