In the last year and a half, possibly two, we've gradually been upgrading our remote servers.
The upgrade has us moving from physical servers to VMs, from Win2003 to Win2012, and from Domino 8.5x to Domino 9.0.1.
We've done this by building new servers using a temporary server ID and then making the necessary changes.
We've had no issues with this.
What I have found over the upgrade period is that sometimes the new server will show up in the ddm.nsf with either a server monitoring message indicating that there is a duplicate document in the events4.nsf, or sometimes a document missing from events4.ntf. Early on, running the command 'tell event clean ($Messages)' would clear the duplicates message. I never knew how to get rid of the missing documents message, but it would go away on it's own.
However, we've finished the upgrades and I've got these messages appearing for 7 of my 8 servers, and that command isn't working.
I tried following the instructions at the end of this link by doing the steps on a server that doesn't have an issue. http://www-01.ibm.com/support/docview.wss?uid=swg21239526
However, that succeeded in 1) adding that serve to the list of servers with a duplicate message in events4.nsf, and in several cases, changing the number of duplicate messages from 1 to 2 on other servers.
I'm at a loss on how to get this resolved.