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Server 2003 no longer PDC. How to clean up?

Hi. Sadly I still have some DC’s that are running Server 2003.
I try to install a piece of software that does not run on PDC’s. So I moved all the FSMO roles to a different DC but the software I try to install still thinks that this server is a PDC.
I think I need to clean the system but have no idea where to start. Has anyone had a similar problem?
Will ntdsutil metadata cleanup break the DC?

So just checking the Roles have actually moved OK. If you run in an Administrative Command Prompt:

netdom query fsmo

On both your new DC and your Old DC does it show the same and does it show the new DC for all the roles?

I’ve had before where I’ve moved the FSMO Roles to a new DC but an old DC hasn’t updated for one reason or another and things reverted or partially reverted back.

Yes, on both server I see the correct information:
Schema owner MainServer.domain.com
Domain role owner MainServer.domain.com
PDC role ServerY.subdomain.domain.com
RID pool manager ServerY.subdomain.domain.com
Infrastructure owner ServerY.subdomain.domain.com
The server that I moved all the FSMO roles from was ServerX.subdomain.domain.com