After a lot of debugging, it turns out that the solution is absurdly simple.
Ensure that the entire "calibre library" folder tree is not read-only.
In windows:
Calibre Portable\Calibre Library>attrib -r *.* /d /s
In other words: open a cmd prompt.
go to your Calibre Library folder
Type attrib -r *.* /d /s
Attrib: Set attributes
-r: Turn or Read-only
/s: do subfolders
/d: Processes directories as well.
Good luck.
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