Really the best solution is to take heavily annotated books to the Reader Library and store them there for further review...
What also helps is to adjust the type of sorting that is applied to the annotations: by entry date always works best for me (should be the default anyway)...
And maybe just maybe, a complete reformat (save everything to Reader Library before and make sure it is there) might always help to unclutter leftovers ranging from deleted book residues to Calibre files to filesystem metadata and so forth...
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