You get these files on a Linux system (such as the Kindle) when a file has been deleted, but another process is still using the file, so that the file can't be permanently deleted. They will disappear automatically the next time the system is rebooted. If you fully shut down your Kindle, and then reboot it, the files should be gone.
Naturally they will not show up in the Kindle's list of eBooks, since they start in a "." which, on a Linux system, indicates that the file is "hidden".