Hey does anyone know if it's possible that phalcon's migrations can backup cronjobs?
No, the migration is just for databases. Cron jobs are held (if you're on a *nix machine) in the crontab (crontab -l). If you want to back these up, then just do something like this: crontab -l > cron_backup.txt to put the cronjobs into a text file.
But it depends. When you say "backup cronjobs", what do you actually mean?