Jobs keep running after the first 100 chunk is done so you can let it run for a while and come back and hit ok to apply the data, let it do its thing and then hit ok on the next batch and so on.
If you have enough memory it shouldn't be too big a deal. I have 4 gigs of memory and let a batch run on 1,000 books and Calibre was eating up nearly 1.5 gigs but I was able to finish. Restart Calibre and then let another big batch run and repeat.
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