How do i smoothly update ntpd's peer list?
Solution 1:
ntpdc can do this for you -- specifically the addpeer and unconfig commands.
Basically update your config file, then use ntpdc to add the new peers and remove ("unconfigure") the old ones (after ntpd accepts the new peers as sane candidates for synchronization!)
You should also consider using a redundant device (routers with HSRP, or unix machines with HA failover/CARP/etc.) as your NTP source, or configuring more than one peer -- You don't want your clocks going insane just because one time server has a problem...