I don't know if this will apply to Kobo, but it might help.
When I update an eBook on my T1, I don't send it to the T1 via Calibre, I just copy the new version over the existing version so all files that contain the information about this book won't be modified. On;y the copy of the eBook will be changed. Then When I go back into the eBook, the T1 keeps me at the page I was in before I updated.
Try just copying the fixed version over the unfixed version and see what happens.
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