I believe a force /scripts/upcp might load them all back again (never tested it anyway) or we could restore it back from a system backup as mentioned in above post. I'd look at a fresh cPanel box which we manage, and these are the root level crons in it (might be useful)
49 2 * * * (/usr/local/cpanel/scripts/fix-cpanel-perl; /usr/local/cpanel/scripts/upcp --cron > /dev/null)
0 2 * * * /usr/local/cpanel/bin/backup
35 * * * * /usr/bin/test -x /usr/local/cpanel/bin/tail-check && /usr/local/cpanel/bin/tail-check
0 6 * * * /usr/local/cpanel/scripts/exim_tidydb > /dev/null 2>&1
30 5 * * * /usr/local/cpanel/scripts/optimize_eximstats > /dev/null 2>&1
5,20,35,50 * * * * /usr/local/cpanel/scripts/eximstats_spam_check 2>&1
45 */4 * * * /usr/bin/test -x /usr/local/cpanel/scripts/update_mailman_cache && /usr/local/cpanel/scripts/update_mailman_cache
15 */6 * * * /usr/local/cpanel/scripts/autorepair recoverymgmt >/dev/null 2>&1
*/5 * * * * /usr/local/cpanel/scripts/dcpumon-wrapper >/dev/null 2>&1
0 */2 * * * /usr/local/cpanel/scripts/shrink_modsec_ip_database -x 2>&1
9 2 * * * /usr/local/cpanel/whostmgr/docroot/cgi/cpaddons_report.pl --notify
30 */4 * * * /usr/bin/test -x /usr/local/cpanel/scripts/update_db_cache && /usr/local/cpanel/scripts/update_db_cache
25 */2 * * * /usr/local/cpanel/bin/mysqluserstore >/dev/null 2>&1
15 */2 * * * /usr/local/cpanel/bin/dbindex >/dev/null 2>&1
5,20,35,50 * * * * /usr/local/cpanel/whostmgr/bin/dnsqueue > /dev/null 2>&1
@reboot /usr/local/cpanel/bin/onboot_handler
09,39 * * * * /usr/local/cpanel/scripts/clean_user_php_sessions > /dev/null 2>&1