--apply refresh does not perform any web requests so this log message is unrelated to the error message above. The error message above is most likely related to updating plex, kodi, discord, etc.
Notify Jellyfin [...]
Network Connection Error: java.net.ConnectException at ...
** --def emby and --def jellyfin are interchangeable and do the same thing
It is however possible for standard output and error output to not be synchronised exactly due to output buffering. You can check the correct sequence of events by checking the log file. You can click on the printer icon in the lower left to check the log file.
In Filebot Node for Synology there is a section named "POst-processing options". In that there is an entry called "Emby" . I filled that entry with the API key retrieved from the Emby Server. I will remoc=ve it and see if the problem is replicated or not. Is that the right thing?