According to that books are being transferred fine, you just aren't able to run the viewer for books on the device. Just view them directlyon the device itself. And this will likely be because the Linux kernel developers recently broke file operations for kindles
https://bugzilla.kernel.org/show_bug.cgi?id=203973
calibre has a workaround for that kernel bug but the workaround has not been applied tested for viewing books ont he device. I encourage you to pester the kernel developers to implement the proper fix I already told them about.