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The disassociation comes from going back and forth between the original mess and my changed mess and the original pdf...if any. I try to catch missing items on the fly to avoid reading line by line with the pdf as much as possible. In line pictures on two column pages create all sorts of problems for people who don't set up the OCR well or check it when it is done. When the text is from the PDF, it is there mostly for search purposes, not for extraction to create an epub document. So they often don't check it as well.
When I have a missing chunk it is often best to use book view to paste text out of a pdf as when you highlight text in reading mode in a pdf, it maintains the columns. When you switch to text view, it often shows the two columns as one line and you can only select two columns at once. Hooray for book view in this instance.
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