You may see this error on occasions when trying to remove a Standard or Enterprise FE pool sever.
Error: An error occurred: “System.InvalidOperationException” “Cannot publish topology changes. Conferences still exist on one or more deleted services.”
Open the lync powershell and run:
From there you will see all conference directories listed, take note of the directories listed under the server you are trying to remove
Then run remove-csconferencedirectory -identity number
number=two digit identity listed in the get-csconferencedirectory command
Now retart the lync services or reboot the server and try to publish the topology again.