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Turn off the option in the viewer preferences to keep a copy of the bookmarks current page position in the ebook file. If that option is on then you will have two programs writing to the file at the same time, which might cause the problem, although since you are on windows, the file is auto-locked and so it should not be possible for simulateous access anyway.
More likely you have some thing else going on. From your description I'd guess the file was corrupted between the time you closed the editor and then re-opened it.
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