Did you make any plugin changes?
Ok, you were right. I managed to fix ipa-replica-manage del command. Apparently, after I restored original .py files I needed to delete .pyc files as well. That fixed the error here.
As for AttributeError: 'ldap2' object has no attribute 'Object' - I applied this https://pagure.io/freeipa/issue/8686 patch since it is supposed to fix the
PKINIT certificate request failed: Certificate issuance failed (CA_UNREACHABLE: Server at >https:///ipa/json failed request, will retry: 903 (an internal error has >occurred).)
error.