IIRC you get to choose which libraries are exported/imported and you can choose whether or not to export/import the configuration folder.
Try it for yourself with a local test library - I assume you have backups, if not see ==>>
How do I backup calibre?
And ==>>
I am getting errors with my calibre library on a networked drive/NAS?
Quote:
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If you [. . .] use a file syncing tool like DropBox or rsync instead of a networked drive [. . . ] it is essential that you make sure that both calibre and the file syncing tool do not try to access the calibre library at the same time.
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BR