@mathil: I'm not sure I understand your question (and/or what exactly you're currently doing. Which covers? Which plugin?)
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The filenames are fixed, and Calibre will always generate all three of them, no matter whether that's done by the device driver during a "Send To Device", or via Kobo Utilities (because Kobo Utilities will in fact just be calling the driver to do the work
).
If you meant: can you ask Kobo utilities to *delete* existing thumbnails, then I don't *think* so, but, again, that's basically the complete opposite of what I'm trying to achieve in my setups, so I wouldn't really know
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(Because, again, Nickel will be generating those after the fact anyway, and they'll quite possibly be larger that way).