Make sure those controllers are not used as Secure Ticket Authority (STA) in the Netscaler Access gateway; if so replace those IPs with the new controller IPs. same goes with Web Interface gateway configuration. – This is very important else you will break remote access.
shutdown and remove the Virtual Machines from Citrix Studio.
uninstall Director that is pointed to this site.
clean up configuration of these controllers from web interface or store front.