Kobo's software is not designed to have books change.
Updating books in Kobo is a several step process and needs the
Kobo Utilities plugin to update ToC as a separate step from sending updated books to the device. For some metadata updates, the standard procedure is to connect, send, disconnect (for Kobo to import), then reconnect again to update those metadata. They have much expertise in Kobo issues in that thread.
(I found it so cumbersome that I switched to using KOReader on Kobo instead and wrote my own glue code in both KOReader and Calibre. I've documented what I did
here, but I'm not at this point supporting it for other users.)