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Zetmolm - I would try giving calibre a dedicated directory for its temporary files via the CALIBRE_TEMP_DIR
Environment variable.
On Windows I have it set to
C:\_AppData\Calibre\Temp.
And, on Windows this 'feature' was introduced a while back, presumably because MacOS has something similar. I suspect on newish systems it's turned on by default.
Added: such features have been known to pull the rug out from under the feet of a long running application. What might make sense on a fiddle-fone OS, doesn't necessarily make sense on a desk/laptop OS.
BR