I don't bother trying to copy stuff back and forth between Kindle and PC. It ended up taking up too much of my time trying fiddle the clippings.txt into some sort of workflow.
I create a quick note (on the Kindle) at the spot where something is wrong (I also tend to include a chapter number in the note). Then I sit down with the source document open on the PC, and my Notes and Highlights open on the Kindle. With the chapter numbers, it makes it fairly trivial to search the source for some nearby text that the Kindle included in its highlight.
I read a few chapters, then fix those chapters in the source, rebuild the MOBI... reload on the Kindle, and pick-up reading where I left off with a fresh, empty clippings file.
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