Whispersync has nothing to do with KOReader, so I'm not sure what you were asking there...
KOReader's own metadata handling is put in the book's sidecar folder (e.g., for an ePub: ${filename}.sdr/metadata.epub.lua). The actual content of the file is portable, it doesn't depend on a specific filename, so you can move stuff around manually without any issue.
KOReader's sync feature can sync *progress*, but not notes/higlihts (AFAIK, I'm not familiar with the details).
You can also use
@embryo's tool to export notes/highlights to more human-readable formats.
TL;DR:
Quote:
Originally Posted by kokaros
Using the stock kindle reader I know that I could just plug in my device, copy the .sdr folder
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Doing just this happens to be portable in KOReader's case
.