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It should finish eventually - remember that it is all about the book formats, and that if you aren't dealing with ePubs then it has to convert to ePub which is where 99% of the time will be spent.
I do intend (once I get feedback on my changes to Extract ISBN) to apply similar changes to this plugin to break up into batches. So if for instance it is batches of 100 books by default then in this case you would presumably be able to have 900 of your results applied and then cancel the last batch which has the problem books in it to subdivide and isolate the problem one(s).
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