We must use PTC's WindchillDS for the upgrade process.
During upgrade, organizations and groups are migrated into Windchill and the entire cn=configuration,cn=Windchill_11.1,o=ptc structure is migrated into JSON files in %wt_home%\IEConf.
Post-upgrade, we must cleanup the DN structure. I would do this in WindchillDS, before export/import into OpenDJ.
1. Delete cn=configuration,cn=Windchill_11.1,o=ptc
Compare the entries in cn=Windchill_11.1,o=ptc and cn=Windchill_12.1,o=ptc to determine where your user accounts reside. They should be in the cn=Windchill_12.1,o=ptc structure, but just ensure they aren't in both.
Check the database to see where Windchill thinks they reside:
select remoteObjectId from RemoteObjectId where remoteObjectId like '%cn=Windchill_11.1,o=ptc';
select remoteObjectId from RemoteObjectId where remoteObjectId like '%cn=Windchill_12.1,,o=ptc';
The goal is to migrate everything to the cn=Windchill_12.1,o=ptc node and delete the cn=Windchill_11.1,o=ptc node.
When cleanup is complete, the only structure remaining in WindchillDS should be the participants (users) under cn=Windchill_12.1,o=ptc.
2. Determine if both Administrative and Enterprise branches are necessary. They are in my environments because I separate organization participants from site participants. But many companies don't bother with that distinction and ignore WinDU when it complains about participants assigned to the wrong domains. If all accounts are in the Administrative LDAP, you could eliminate the EnterpriseLDAP branch and JNDI Adapter.
3. Ensure the upgrade Site Administrator account's name is wcadmin and no longer includes 'Administrator' as a second name. Also ensure 'wcadmin', and not 'Administrator' is used in site.xconf.
4. This is the last upgrade that will mess with LDAP entries. So, when continuing forward with OpenDJ, I clean up the structure to remove the Windchill version from the DNs (cn=Windchill,o=ptc). Export the LDIF, use search and replace in the LDIF file, and then import into OpenDJ. On the DB side, update all DNs (SQL Server command): update RemoteObjectID set remoteObjectId=replace(remoteObjectId,cn=windchill_11.1,o=ptc,cn=windchill_12.1,o=ptc) where remoteObjectId like '%cn=windchill_11.1,o=ptc';
When migrating to Active Directory or any other corporate LDAP, the entire nodal structure changes anyway.
At this point, the entire structure should only have user accounts in it. Now export from WindchillDS and import into OpenDJ.
https://www.ptc.com/en/support/article/CS392017
https://community.ptc.com/t5/Windchill/who-is-using-V3-ldaps-other-than-WCDS11-2-for-windchill-12-0-1-x/m-p/797478#M66922
Only OpenDJ should be running and Windchill should start without issue.
FYI: For OpenDJ, I use "cn=Manager" like PTC did with WindchillDS.
https://community.ptc.com/t5/Windchill/Problem-Installing-OpenDJ/m-p/939834#M79374%3Fsource=search
