Where are you copying the books to? I would suggest creating a directory in the root of the exposed volumes (call it ebooks or whatever other name you like) and copying the books into there. Avoid directories with a '.' as the first character since those are Linux hidden directories and likely to be skipped. Some other directories such as most of the ones in the .kobo directory will also not be scanned.
Did you see the black screen with the importing books bar running across the screen after you safely eject? If not, your Libra Colour is not seeing the books to import them.
Please note that if your Kobo can not locate the books to import them, the database will not shown them as present when you reconnect. On the send, calibre shows them as on the device since they were just sent but have not yet been imported to the database.
Where the books will be sent from calibre depends on the template on the first page of the configuration pages for the KoboTouch/KoboTouchExtended driver. My personal use template is:
Code:
ebooks/{author_sort:sublist(0,1,&)}/{title} - {authors:sublist(0,1,&)}
To break down the template, ebooks is the name of the directory in the root of the exposed storage while {author_sort:sublist(0,1,&)} creates a directory based on the first entry in the author sort list. The {title} - {authors:sublist(0,1,&)} creates the name of the ebook file based on the book title with the first author in the author list. Both the first entry items are to keep the filenames/paths within limits given that I have quite a few anthologies with more than 15 authors and the paths and filenames exceed the limits that calibre imposes for compatibility.
Sample would look like:
ebooks/Flint, Eric/1633 - Eric Flint.epub