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CC does not play well with USB connections. You should use one or the other.
Assuming the "scan on connnect" option is checked (and it is by default), when you connect as a wireless device CC will look for new books in its folders. If it finds some then it attempts to extract some metadata, adds the books, and then sends the books to calibre for analysis. Calibre will attempt to match the books with books in your library and will send back correct metadata. By killing calibre you interrupted the process, leaving CC with books with bad/incorrect metadata.
The way to fix it is to connect CC as a wireless device and let the process finish. The analysis phase can take a long time.
What version of CC and what version of calibre are you running?
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