I don't normally delete from my Kobo Touch using calibre. Actually, books normally stay on the KT forever. Anyway, I just did a couple of quick tests. I am seeing the same thing. The list of the books on the device is not being updated either.
I've actually been looking at this code, and this not happening might explain something else I am seeing. The problem isn't related to the firmware version, or at least not a recent version. I didn't think there any changes in the Kobo driver code that would account for this. But, it might be a change elsewhere that hasn't been reflected in the driver properly.
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