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With regards to the Kobo filesystem not being cleanly unmounted before connecting to PC, I just realized, there is one variable to my Kobo that is non-standard and I did not test against.
I have, in the past, installed the hak to auto fill series data when books are imported. It's a subtle thing and persists across firmware upgrades.
When I have time later, I will factory reset a Clara HD and test 4.31 from a clean factor install, and if the error does not present itself, will try install that code again and see if it makes a difference.
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