I've set the following to set a key size of 4096 on my Letsencrypt certificates;
/usr/local/psa/admin/conf/panel.ini
[ext-letsencrypt]
renew-before-expiration = 45
rsa-key-size = 4096
check-domain-cert-authority = true
According to the manual nothing has to be restarted but the key size does...