UPDATE:

I have resolved the issue. The problem all stemmed from the 

$getcert list 

Having expired certificates. I had to startup IPA using 

ipactl start --ignore-service-failures 

and then issue the 

getcert resubmit -i <<request id>>

One certificate came up as CA_UNREACHABLE but had a valid expiration date in 
the future. I rebooted the VM and everything is working now. 

Thanks for all of the help but it is concerning that these do seem to break. I 
have added a login warning prior to an O/S upgrade or reboot to check that the 
certs are all valid.
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