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According to your .json, you never deleted the 00,01 and 02. They were last saved while "checked". You saved no other library names.
Please do this:
Exit from Calibre.
Delete the .json while Calibre is not running.
Run Calibre.
Start CALM.
Go to the Source Library Tab.
Do not click on 'load all known libraries'.
Manually enter the Library names you want. Save.
Exit from CALM.
Exit from Calibre.
Upload the .json so I can see it.
Thanks.
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