My situation is that we have production unix scripts that ftp files over to a windows server. I'm not sure if its a 2000 or 2003 server as I dont work on server, more on the unix side. It turns out that they are changing servers on the network. So they are migrating our data over from say Server 1 to Server 2. This will cause us to have to change our scripts to now point to Server 2. Is there anyway that a systems admin on their side can create an alias/pointer name to Server 2 using the Server 1 name, so in conclusion we wouldnt have to change our unix scripts. Or can we create an alias on the unix side to point to Server 2 where any script would reference Server 1? Thanks in advance.

I'm not sure, if I understand you clearly.

If there is hostname usage in scripts (DNS names) you could use "/etc/hosts" file (or equivalent) on your server to override hostname <-> IP assignment:
The disadvantage of this resolution is that physical Server1 will be not accessible via DNS name.