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This bug is created as a clone of upstream ticket:
https://fedorahosted.org/freeipa/ticket/2148
The proxy script failed to do is update the security domain entry stored in ldap for the master. This leaves the ports as 9xxx so if you go to create a clone against that server you'll get an invalid clone_uri error.
You can fix this by going into ldap and changing the relevant security domain entries for all the CA's that have been converted to use the proxy to use the proxy ports instead. They will be under ou=security domain, $basedn. They will basically all be 443, except for UnscurePort which will be 80.