Hello,
is there a possibility to save the pdf certificates automatically while the user is generating them? in the old plugin there was a option so save them.
Sorry, that is not possible at this time. There is an issue for that, see https://github.com/markn86/moodle-mod_customcert/issues/38. If you want to provide a patch or if you have a developer available who can create a patch that would be awesome. Cheers.