Look for entries in the /var/log/dirsrv/slapd-EXAMPLE-COM/errors file like:

[13/Apr/2012:16:33:34 -0400] NSMMReplicationPlugin - ruv_compare_ruv: RUV [changelog max RUV] does not contain element [{replica 1181 ldap://server1.example.com:389} 4f5048b70000049d0000 4f50e8710000049d0000] which is present in RUV [database RUV]

We need to run the CLEANRUV task for entries that match the replica ID which is 1181 in this case. Here is a sample ldif file:

dn: cn=replica,cn=dc\3Decg\2Cdc\3Dmit\2Cdc\3Dedu,cn=mapping tree,cn=config
changetype: modify
replace: nsds5task
nsds5task: CLEANRUV1181

The number after CLEANRUV is the replica id from the logfile. The dn is obtained by running:

ldapsearch -xLLL -D "cn=directory manager" -W -s sub -b cn=config objectclass=nsds5replica

You also need to clean the PKI LDAP directory which runs on port 7389 and uses o=ipaca as the baseDN i.e.

ldapsearch -xLLL -D "cn=directory manager" -W -b o=ipaca  '(&(nsuniqueid=ffffffff-ffffffff-ffffffff-ffffffff)(objectclass=nstombstone))' -p 7389 -h localhost

Once you have obtained the replica IDs which need removing from the logfile, you can use the following ldif to remove them:

dn: cn=replica,cn=o\3Dipaca,cn=mapping tree,cn=config
changetype: modify
replace: nsds5task
nsds5task: CLEANRUV1181

The replica metadata is not replicated to the other servers so you need to check the log files and run the CLEANRUV tasks on all replica servers.