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When you select "Keep reading" it doesn't actually mount to the PC so you don't need to eject it (it won't show up as a drive to eject).
Most of the books on Kobo also have a "Download EPUB" option (not all books do, but that's rare) - you can download these using ADE as a backup. The kepub format is specific to the Kobo database and as far as I know, you can't read them anywhere else whereas the EPUB is more universal.
If you download Calibre, you will be able to see the preloaded books and can decide which ones to delete that way (you can also individually delete them on the reader, but that would probably be tedious). All the preloaded books are public domain so can be found elsewhere on the web if you do delete them and want to get them back.
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