Deleting retention.dat won't cause any issues as it will be recreated. The purpose of the file is to save service state information across reboots or restarts of the nagios service. You could simple rename the file rather than removing it: mv /usr/local/nagios/var/retention.dat /usr/local/nagios/var...
Are you looking for direction on creating crontab entries for your command or are you asking which command is preferable? If the latter, if I understand your backup methodology, either command would work as for your backups the created timestamp and the modified timestamp would be the same. Let us k...