Having only the most rudimentary understanding of how e-ink works you are probably stuck with it.
On my Kobo Wi Fi there are two micro-capsules/pixels or whatever that are permanently stuck as black pigment. They don't look like LCD pixels at all though. They look like two little flecks of ink that got on the page when the book was printed. Sorta.
Not sure if that is that same as what you are seeing or not. On the Kobo, it is permanent.
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