We had a secondary domain that was used for GroupWise Libraries, this died
a horrible death recently but as it was no longer in service we didn't
worry. It has been removed from the primary domain and NDS along with all
its objects.

However, and I'm sure this is because they way it was removed, the
libraries still show up in the client when the user is using Tools, Find,
Find by Example, Item Item Type = Document, Library selector. We do have
libraries on the primary as well that are still in use.

Does anyone have any idea how I can get the primary domain to stop seeing
these libraries.

We are not able to bring back the secondary.