Of course.
Copied as root, huh.
Well, why did you restore them using sudo???
`cp` by default does not preserve ownership, in order to preserve ownership you should use `cp -rp` or `man cp`.
Honestly, I am surprised *anything* worked.
I *cannot* predict everything you might do. This ^^ was important infomation.
*
I assumed if you were restoring files from a backup you were recreating them as the current user. Why would you *want* to use the previous owner, it might not even be the same as the current owner... just a bad practice to get into.
Well, now you know for next time.
* -- Next time I help someone, I may just have to suggest a preliminary `sudo chown -R $(whoami): ~/.config/calibre && chmod -R u+rw ~/.config/calibre` on general principle. Thank you 