I didn't get the chance to clean anything up because there's truly nothing 
there:

root@ipa pki]# pwd
/var/lib/pki
[root@ipa pki]# ls
[root@ipa pki]#


[cid:image001.jpg@01D1BDEA.06FFA830]<http://www.high5games.com/>
Daniel Alex Finkelstein| Senior Dev Ops Engineer
dan.finkelst...@h5g.com<mailto:dan.finkelst...@h5g.com> | 212.604.3447
One World Trade Center, New York, NY 10007
www.high5games.com<http://www.high5games.com/>
Play High 5 Casino<https://apps.facebook.com/highfivecasino/> and Shake the 
Sky<https://apps.facebook.com/shakethesky/>
Follow us on: Facebook<http://www.facebook.com/high5games>, 
Twitter<https://twitter.com/High5Games>, 
YouTube<http://www.youtube.com/High5Games>, 
Linkedin<http://www.linkedin.com/company/1072533?trk=tyah>

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From: Rob Crittenden <rcrit...@redhat.com>
Date: Friday, June 3, 2016 at 17:47
To: Daniel Finkestein <dan.finkelst...@high5games.com>, 
"freeipa-users@redhat.com" <freeipa-users@redhat.com>
Subject: Re: [Freeipa-users] FreeIPA 4.2.0 on CentOS 7.2 as replica of FreeIPA 
3.0.0 on CentOS 6.8; cannot install CA components as replica, cannot promote to 
master

root@ipa ~]# pkidestroy -i pki-tomcat -s CA

ERROR:  PKI instance '/var/lib/pki/pki-tomcat' does NOT exist!

The IPA installer is looking for the existence of
/var/lib/pki/pki-tomcat/ca/conf/CS.cfg. At least some things in
/var/lib/pki/pki-tomcat are links to /etc, notably alias and conf. You
can try manually cleaning those up.

rob
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