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I also get occasional failures of the restructuring algorithm but usually it’s due to malformed coding in the epub and is easily fixable. I would ignore the whole Borkify issue until you get it to pass the restructuring.
When you first open the epub in Sigil hit F7 to run a well-formed check. That should give you a list of problems to fix. When fixed you should be able to restructure, then Borkify (if you still need to).
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