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My workflow is similar to DiapDealer's.
I proof a MOBI format file and make notes my simply moving the cursor to the offending area and typing some often cryptic note indicating the error. When back at my PC, I open the book on the Kindle and View Notes & Marks. The Kindle shows a short block of text around the annotation and my note. I open the source document, usually an epub at this stage in the proofing, and use search and replace to find the section of text to correct.
I find this easier than attempting to sync with Kindle for PC or simply using a copy of the Kindle device's clippings.txt file and its Locations references to manually find the same section of text in Kindle for PC. These methods still require that you do a S&R in the source text to find the matching position.
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