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What kind of device are we talking about here?
Keep in mind you *cannot* mix a SmartDevice (i.e., wireless) library root with a standard/wired/USB library root. (Basically, you can't tell two different calibre drivers to use the same library).
On our side, the calibre plugin should have shouted very sternly at you if you tried to set your inbox at the root of a library that was already being used by another calibre driver.
Once you take care of that, IIRC, the search plugin will happily parse multiple libraries at once, I think?
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