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Originally Posted by DrChiper
All my books are EPUB ones and touched-up by calibre before sideload.
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Not sure what "touched-up by calibre" means. Are you doing a conversion, Polish, edit or something else? Or do you just mean calibre's metadata update during the send?
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Never had any problems with them before.
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Well, that's the point. Something has changed that is causing the behaviour. Unless you have changed what you do with the books, then it is in the firmware. I'm not seeing the problem and have not changed what I do with the epubs. I am using kepubs a bit more, but, for epubs that I read, there is no difference and no problems. That suggests there is something different about your books, and mine. And @jackthereader and mine. And that something has changed in the firmware that is being triggered by these differences. Without knowing what the differences are, it is very hard to work out how to fix it.
The only change I can think of recently that might be responsible is that Kobo have been changing some things with the ToC handling. And the reading position and annotation locations are actually relative to the ToC entries. A problem in the ToC, or something unusual, might be the cause. But, without seeing an example that does cause the problem, it is impossible to tell.