Great, well done.
I think I have also found the problem. I’ll try to explain it.
When I RE my RE settings were the same as I would use for a whole DB RE, so I am getting Entities (the one I selected) also Users, User Groups and Tablespaces. There are no other items in the RE database.
In the Convertor I selected only Entities checkbox (and its children).
I then deselected the bits I didn’t want (leaving the new entity) and performed the merge.
This is a representation of what I think is happening;
We have a User Group (UG1).
In my target model the only member is USER1 (since we have a seperate model for each schema).
My target model knows about other (deliverable) users, eg USER2, USER3.
In my RE’d model I also have development/test users, eg DUSER, TUSER.
In my RE’d model UG1 has all the above users (USER1, USER2, USER3, DUSER, TUSER) as members.
After the merge, my target model UG1 has users USER1, USER2, USER3 and 2 errors are raised (DUSER and TUSER).
I looks like the merge is trying to merge User Groups, though they were not selected for the comparison.