Transactional replication challenges.

Hi, I have a problem that I have run into with SQL transaction replication. I
work for an ASP that hosts an oracle application called JD Edwards Enterprise
one.

When updates are applied (ESU) to the app, any DDL statements that run that
add or alter indexes or columns fails with a marked for replication message.
Only way around this that I can see is to drop the publication and
subscription and recreate it.

Using the snapshot is not an option due to limited bandwidth, T-1. The
entire database is replicated and is 150GB. With that being said I also will
need to get these changes over to the subscriber database. Is there any other
way to do this without dropping the publication?

Ideally I would like the application to make the changes instead of manually
running the sql statements. But I don’t know if this is possible. Biggest
challenges I see is getting this to work without having to do a manual
resynchronize replication subscriptions.

Replication was setup using KB320499.

SQL 2000EE SP4
Windows 2003 EE SP2

Server A, Publisher with push subscription, Seattle
Server B, Subscriber , Georgia

Thanks for your time.