I had to replace my HD but had Calibre library on back-up. When I reinstalled Calibre it saved most of the settings but I had reinstall the plug ins. I must have had it set to "only selected books" before but default must be whole library as that is what it was doing. Lot of stuff you take for granted until disaster strikes. Even with a back-up no walk in the park to reinstall your OS, all the updates, applications. Also your back up sometimes puts things in the wrong place so stuff has to be moved around. I am on day 3 of this debacle.
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