From what you’re describing, it seems you have an NT domain and AD domain with separate accounts.
So unless that’s not true and your EX 5.5 & EX 2K3 Servers share the same service account, changing one should have no bearing on the other one. Just make sure you stop all the EX 5.5 services first and warn the user in advance of downtime.
Though is not your problem, but running EX 5.5 on a DC is a definite NO-NO! Is EX 2K3 running on a DC too?