Addendum - Although the pilhole-g command does work, it's slow and puts extra strain on the main block list servers.
An alternative (and much faster) way of refreshing the lists can be done by disabling and re-enabling pihole or as @jfb suggested, a pihole-FTL restart.
Example pihole restart cron:
0 7 * * * root pihole disable && cat /etc/pihole/regex.list.standard > /etc/pihole/regex.list && pihole enable
0 23 * * * root pihole disable && cat /etc/pihole/regex.list.extra >> /etc/pihole/regex.list && pihole enable
Example FTL restart cron:
0 7 * * * root cat /etc/pihole/regex.list.standard > /etc/pihole/regex.list && service pihole-FTL restart > /dev/null 2>1&
0 23 * * * root cat /etc/pihole/regex.list.extra >> /etc/pihole/regex.list && service pihole-FTL restart > /dev/null 2>1&