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Hi Bronwyn welcome to MobileRead.
I haven't experienced your problem - the only time I have ever lost my bookmarks was before the upgrade when Kobo needed recharging. It would just die and after I recharged the book mark was always where I had been up to the previous time I shut down.
Maybe some more information could someone come up with an answer for you.
How are you shutting down your Kobo? Are you actually shutting down or letting it sleep and then shut off automatically?
Also what type of book are you are reading? Is it happening just with one book or with all of them?
Have you tried Kobo customer support? They do take a while to respond sometimes and you often get a fairly generic response but they may be able to help you.
Good luck.
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