Have you ever added a Front End server into your topology using just the server name (i.e. Server1) and not the fully qualified domain name (i.e. server1.domain.local)? I have without thinking and published the topology. Easy mistake to make when you are not concentrating. However, you would think that undoing your mistake would be straightforward by removing from the topology and republishing. If you try this you will get an error saying that you cannot remove the server because it contains conferencing data.
To allow the server to be removed you need to delete the conferencing directory first.
First you need to grab the right conference directory identity for the server
The identity will be an integer e.g. 5
Then remove the conference directory using
Remove-CsConferenceDirectory –Identity <5> -Force
Once this has been removed you will be able to remove the server from the topology and re-add correctly.