Strange. I've never had those issues with 3 different Kobo models. Of course I sideload and manage everything on my Kobos with calibre and wifi is always off. I've found that this works best. No missing covers, metadata is maintained automatically (including collections and series grouping), reading status is backed up automatically too and can be restored to the device with one click if needed. No syncing issues (as I never sync). In short, pure bliss.
YMMV, as always.
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