Quote:
Originally Posted by _kind_le
I have similar problem but with books from amazon store. "My Clippings" file has highlight records for them but nothing in the books. .sdr folders are there and I'm pretty sure Calibre was not managing them.
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My Clippings is not 'source of truth' for annotations. As @Quoth says it is just a log file and is not indicative of current annotation state. If book does not show annotations there are not any.
If you are in habit of side loading amazon content with calibre and staying offline while starting to read and annotate, then it could be that sync is 'restoring' empty annotation state when you do connect because it thinks this is 'newer' somehow. Perhaps this can occur with direct downloads as well if you disconnect before starting to read and annotate, then stay offline for awhile.
(it seems similar to 'disappearing covers' issue some people have had. I've never been able to reproduce that but being offline for days/weeks may be a contributing factor from what I can gather from reports)
You can verify sync is working properly by using read.amazon.com to open amazon books and see if your on device annotations are getting backed up. And you can make annotations there and verify they get synced to device.
Side loaded (non amazon) content annotations are not backed up anywhere of course.
But would really need more detail from you to troubleshoot this.