If you are planning a upgrade from 2003 to 2008 AD, then you'll have to take one DC offline and run a Metadata cleanup of the DC you took out. If/when the upgrade goes fine, you can never add the "offline" DC back in.

(If you're extending the schema all DCs needs to be online).

If this is what you are doing, I think this is not a risky job that's worth doing the above task...

Thanks for the replies, yes, we are migrating from 2003 to 2008 R2, we have a couple of critical custem apps that we can't test in the lab in advance, so we need to have a backout plan in case any application stops working,

We only have one domain with 3 domain controllers

Still no one answered my question by the way, thought I will repeat it :D

"as far as I understand nothing changes at the client side, am I right? "

to explain, let's say I virtualize the 3 DC's and turn the physical ones off, do the upgrade using the virtual servers and if an application stops working turn the new set of DC's off and start the old 3 DC's, should this work? or some of the colients will stop working with 2003 after the migration?

Do the custom apps have any custom domain partitions (application partition)?

The vendor of those apps should be able to say if a schema/domain upgrade will affect their app.

Like Mike says, introducing 2008R2 DCs is a "routine" job. If your DCDIAGs are clean and the app vendors say go, you're doomed to succeed :)

"as far as I understand nothing changes at the client side, am I right? "

Correct.

If you have VM hosts you can make a lab and do the testing. Leaving the prod.environment up and running.

We know nothing about how these apps work, and there is no one to support them, we've tried to move them to the lab with no success, so our only option is to move ahead and rollbak if they stop working

Thanks Snusgubben, are you assuming... talking from experience or do you have any official source?

Can any one confirm that clients are indpendant from the version of the AD?

Did those apps make any schema modifications?

* assuming you don't have any NT4 clients

Thanks everyone for the wonderfull support