I've had a short conversation about this in irc channel, but figured I'd open a ticket to keep a track of things.

We are trying to reinstall a replica (replica-x1) but it errors out with the above error message. The logs of ipa-replica-install.log are below
I've tried following a similar issue here
Re: [Freeipa-users] Error setting up Replication: ldap service principal


but am having problem executing a command as suggested by Ludwig.
I'm trying
db2index.pl -D cn='Directory Manager' -v -w - -t entryrdn

on the server.pop.domain (source server) but that just gives --help message. 
At any rate speaking to Rob this may not even be the correct step to take.
PS: I have made sure to uninstall the original replica and also ipa-replica del replica-x1.pop --force on the source server.
2018-01-05T21:23:57Z DEBUG Process finished, return code=0
2018-01-05T21:23:57Z DEBUG stdout=add objectclass:
2018-01-05T21:23:57Z DEBUG stderr=ldap_initialize( ldapi://%2Fvar%2Frun%2Fslapd-DOMAIN-LOCAL.socket/??base )
2018-01-05T21:23:57Z DEBUG   duration: 0 seconds
2018-01-05T21:23:57Z DEBUG   [5/7]: enable GSSAPI for replication
2018-01-05T21:23:57Z DEBUG flushing ldaps://replica-x1.pop.domain.local:636 from SchemaCache
2018-01-05T21:23:57Z DEBUG retrieving schema for SchemaCache url=ldaps://replica-x1.pop.domain.local:636 conn=<ldap.ldapobject.SimpleLDAPObject instance at 0x74bd098>
2018-01-05T21:24:00Z DEBUG flushing ldaps://server.pop.domain.local:636 from SchemaCache
2018-01-05T21:24:00Z DEBUG retrieving schema for SchemaCache url=ldaps://server.pop.domain.local:636 conn=<ldap.ldapobject.SimpleLDAPObject instance at 0xb76f128>
2018-01-05T21:24:03Z DEBUG Unable to find entry for (krbprincipalname=ldap/replica-x1.pop.domain.local@domain.local) on server.pop.domain.local:636
...
...
2018-01-05T21:27:37Z DEBUG Unable to find entry for (krbprincipalname=ldap/replica-x1.pop.domain.local@domain.local) on server.pop.domain.local:636
2018-01-05T21:27:39Z DEBUG Traceback (most recent call last):
2018-01-05T21:27:39Z DEBUG   [error] RuntimeError: One of the ldap service principals is missing. Replication agreement cannot be converted.
2018-01-05T21:27:39Z DEBUG   File "/usr/lib/python2.7/site-packages/ipapython/admintool.py", line 171, in execute
2018-01-05T21:27:39Z DEBUG The ipa-replica-install command failed, exception: RuntimeError: One of the ldap service principals is missing. Replication agreement cannot be converted.
root@replica-x1.pop.domain.local: /var/log/ipa$