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If you copy/merge the koreader folder over the existing one, you can retain the settings and additions you may have added to koreader, like dictionaries, and fonts. Deleting the old folder before updating looses any such adjustments, including where you have set the reader.lua program to have File Manager open.
I use a hidden folder on my external uSD card, for my library so I have reader.lua /mnt/sd/.Koreader/Books/ as the argument passed to the program. Because I use the KSM to launch Koreader the call is in /.kobo/kbmenu/onstart/koreader_kobo.sh
Not sure how AdvBoot calls Koreader.
Luck;
Ken
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