I got it resolved - IPA does not seem to support importing a rechained external 
CA. It doesn't seem to have anything to do with ipaCertSubject being unique but 
it's something else where there are two different chains for the same external 
CA.

I was able to ldapdelete the old problematic certs from ldap> etc > ipa > 
certificates. And then I was able to successfully run the ipa-advise script for 
adding the CA certs. This time ipa-cacert-manage worked without throwing the 
public key info mismatch error. 

And then I ran ipa-certupdate on all Ipa servers, and clients that required 
smartcard auth. And it seemed to work fine for the new certs. Unfortunately, 
this likely means that the cards with the old chain will stop working but they 
are in the small minority and we'll likely have to get them new cards signed by 
the external CA with the new chain. 

I would like to suggest that the ability to rechain and have two different 
chains for the same external CA be added to FreeIPA. It's likely a rare 
situation but it happens. 
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