Thank you
Quote:
Originally Posted by ownedbycats
Just for documentation, I just updated a fanfic where I had some text highlighted with Calibre's new annotation feature. (Storing annotations inside the ePub is disabled.) It added the new chapter and didn't touch the annotation whatsoever. 
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Also, it seems that glitch I had with the reading position getting shifted upon ePub update no longer happens.
No lost/shifted annotations, either. I suspect it would happen if annotations were embedded and the update is set to overwrite the ePub. I think Kovid mentioned that annotations are stored in a few places though so it might be able to recover.