kodi has an upgrade process to upgrade from 16 to 17.
i've done several tests and it worked in my case.
perhaps something wrong with your plugins.
All the kodi data are in .kodi. First, you should try to boot with a new config to confirm it works : on the batocera main menu, press f1, rename .kodi to .kodi_16, start kodi and confirm it works.
now, the question is why the migration did not work in your case. In the worst case, it's better to start from a new configuration, but otherwise, the file temp/kodi.log should help you.