SIP does not apply for me. It starts with OSX El Capitan (10.11) and I have Yosemite (10.10) installed.
And yes: I deleted the .json file while Calibre was not running. I can see if the file is there, because I have opened up a window where I can see all the files of calibre preferences in real time. You are right: deleting the .json file while Calibre is running does not work. I noticed that after I did some trials.
My suggestion that it is maybe an OSX issue comes from the fact that I had the same problem with the machine of my wife. I thought on paths issues or something like that. So, if you thing it is not an OSX issue, what then? What could I try next?
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