Originally Posted by DoctorOhh
The data from any connected device whether via CC or USB use the same two files to store info, metadata.calibre and driveinfo.calibre so when connected via USB it will know what is already on the device from its library. Now how long it will take on first hook up I have no idea. Connect it and see.
CC does not use the metadata.calibre and driveinfo.calibre files.
When you connect via MTP, calibre will scan the device and presumably find the books that were placed there by CC. Calibre may or may not recognize that the books came from calibre because book matching requires accurate metadata inside the book, which may or may not be there. CC uses calibre's metadata instead of the book's metadata, so book matching in calibre is usually more accurate.
Three things must happen for CC to know about books places on the device by calibre:
1) calibre must have placed the books in the folder that CC uses for that book format.
2) CC must have the option "Scan on connect" selected.
3) You must connect CC to calibre as a wireless device so CC's scanning will happen.
It is probably not a good idea to use both CC and MTP connections on the same device.