I inherited a network in which several DCs are offline and were not removed from AD. Currently, I have two DCs: SVR01 which is the primary DC and BFBACKUP which is the secondary DC. BFBACKUP was turned off for a few days (due to heating issues in the server room). I turned it on yesterday and was hoping that the AD replication would take place without a problem. However, when I looked at BFBACKUP's Computer section (Active Directory Users and Computers), it doesn't have several workstations listed. I checked to see if there were any errors in the Directory Service of Event Viewer, and there is a lot of Error Event ID 1311 (The Knowledge Consistency Checker (KCC) has detected problems with the following directory partition.)
How can I force SVR01 to replicate to BFBACKUP? SVR01 tries to replicate to several of the offline DCs and returns error messages. My thought was to ensure that AD on BFBACKUP is up to date. And then at a later date, I can remove the other DCs.
Use Active Directory Sites and Services to force replication. If that doesn't work, you might want to do what @ErikA suggested. Here's the KB on removing the metadata.
Honestly I would keep BFBACKUP offline for the time being and install a clean Windows server and dcpromo it. If you can't do that, Reinstall Windows on the BFBACKUP server and then run dcpromo.
Once you have two healthy domain controllers, go through the process of cleaning up your metadata using
ntdsutil.I'm with EricA and Nixphoe on this one. You know that you already have metadata cleanup to do so why bother trying to fix BFBACKUP? Wipe it out, setup a new DC, and cleanup metadata for all of the orphan DC's.