I need to apply windows updates to a group of connection servers and was wondering can I apply win updates and reboot one and not mess up the replication between the group? I would like to continue to service desktops during this time.
yes you can, as long as you let them replicate between updates.
another thing, make sure you are working with "direct connections" and not "tunnel".
if you have tunneled connections a reboot will break all those connections to the desktops.