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Found the problem. I was having problem with my icons, so I had uninstalled calibre (and reinstalled after rebooting). But before installing again, I used my shortcut to run from source. At that point, I had only calibre 32 3.48 installed.
Even after I reinstalled calibre 64 4.6, the association remained with calibre 32 3.48, hence the error.
All good now! Thanks for the hints, @davidfor and @kovidgoyal.
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