I'm sure there's something that I'm missing. When I try to move the file that I would tap on to open the book, the file at the new location ends up missing metadata and is often not open-able.
I guess the metadata and reading progress is stored outside the actual EPUB/PDF/etc, and so I look for it by connecting my Kobo to my computer with USB.
Immediately I find that what I'm seeing on my computer, and on my Kobo, are completely different. Even though I have turned on displaying hidden folders, there are just some folders on the Kobo that aren't there on the computer. Also, my books seem to be at the root directory when viewing from the computer, even though it's clear on the Kobo that they're not.
I think I'm going insane

Thank you for your time!
(Please don't hesitate to ask for demonstrations of this because I don't know if I've described it very well)