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I won't be able to describe clearly how this happened, unfortunately, but I remember vaguely I've had a similar experience where I may have clicked inadvertently the button "Queue all books for backup" in menu Library -> Library Maintenance -> Library metadata backup. Picture this happening on a large library: that can run for days and it seems there's no way to stop it.
One has to be very inattentive to hit such a far down button in the menu structure, but sometimes I can be very scatterbrained. Or maybe it was just me changing some custom columns and that can trigger the metadata backup process?
If I recall correctly, I had to use a metadata.db backup to have Calibre running fine again. This happened about 4 months ago. Also, one thing I'm sure is that I wasn't fiddling with RL plugin at that time.
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