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This bug is created as a clone of upstream ticket:
https://fedorahosted.org/freeipa/ticket/3805
I update to F18 my old ipa server that has been upgraded since F15.
It has stil a separate directory instance for the CA.
When certmonger decided to renrew the CA certificate renew_ca_cert failed to update the CA instance users with the renewd certs.
the reason is that renew_ca_cert tried to perform all its operations against the main IPA instance and not the CA instanace on port 7389 where these objects actually are.
all renew_ca_cert operation terminated with 'no such entry' until certmonger failed to update certs as the RA certificate didn't match the cA user anymore.