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I just got a new Severe threat alert, again on a temporary calibre folder. I opened the folder and I saw a lot of filesystem activity in it: files were being added and removed at a fast rate.
The operation that Calibre was doing at that time is full-text indexing, on "fast" mode. After indexing finished, there are no files left, except some *-render-html folders, all of which are actually empty. Accordingly, Calibre now reports "all book files indexed".
So can it be that a couple of EPUB and PDF files (possibly the same ones in the screenshot on previous post) are somehow taken to be "infected" files by Windows Defender as Calibre reads and indexes them?
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