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i don't use import myself but I am pretty sure that a single import completely replaces the calibre config folder, with the version that was exported. In that config file is the name and location of the imported library
so the 2nd import is overwriting the config file that the previous import created.
you should be able to workaround it though,
1.import 1st library then move it to a different folder to keep it safe from what you are about to do next:
2.import 2nd library. ( that will destroy the pointer to 1st library but will not destroy the books in it )
3. use add library to locate and connect to that ( moved) 1st library
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