EnderFrags So the medium in the Internet. At night the MoodleBox goes online. And it is not a "synchronise", rather a nightly cloning of courses, which you develop on a MoodleCloud site.
Well, it is straight-forward, if you have control over both sites:
a) Back up the courses in the original, there is a automatic backup feature in Moodle, to a directory which is accessible via "FTP" (SFTP, SCP, RSYNC, ...)
b) Per cronjob in the MoodleBox fetch those backups
c) Restore those course backups in the MoodleBox. To automate that you might need to install moosh https://moosh-online.com/ on your MoodleBox.
I don't think MoodleCloud https://moodlecloud.com/ allows steps a and b. It is a packaged Moodle, not the DIY Moodle. Check with them https://moodle.org/mod/forum/view.php?id=8277.
Whatever, all those are generic Moodle or Linux system administration. I would try the Backup and restore forum on moodle.org https://moodle.org/mod/forum/view.php?id=746.