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I could be done any number of ways.
theducks' method will create two separate functional libraries, one on each stick, than can then be imported into a single library on a second computer or used as-is as two separate libraries. This works whether you are moving the library to a new machine or simply using libraries on the sticks with the old failing machine.
A second method could be use if you are either moving the library to a new machine or wanting to create a backup archive while you still use the library on the old machine. This method would be to manually copy roughly 1/2 of the folders in the calibre library onto one stick and the other half along with the files at the top level of the library folder onto the second stick. You would have to manually create an empty library folder on the new machine, or the old one after losing its library to a data error, and then copy the contents of each stick into that library folder before the library can be accessed. You should also copy the applications settings to a separate folder on one of the sticks.
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