I need you help!!

There are 2 NW 6.0 servers in main site and a NW 4.11 in remote site and
two locations are connected by ISDN with IP and IPX. Sooner, the IPX
protocol will no longer to be supported for communication between two NW
6.0 servers in one location and a NW 4.11 server at another site due to
ISDN connection is going to be replaced by VPN tunnel(IP only). My
question is how to stop(remove) the NW 4.11 server to try to communicate
with another two servers (NW 6.0)through VPN so that the error message
of “Unable to communicate with server .SERVER3.SHOUT.MAIN” will not be
generated while IPX can not be used to communicate. It’s fine having no
communication with IPX between two locations. Do I need to think about
remove NW 4.11 replica from the two NW 6.0 two servers or remove the
server subject from eDirectory? One of the NW 6.0 holds master replica.
Please advice me how to approach or the steps of how to do and on which
server. Sorry I have no clue at all.

Thank you for any help!!