You may notice that Microsoft Application Virtualization (App-V) Publishing Servers are automatically removed from a Microsoft App-V v5 client by System Center 2012 Configuration Manager.
App-V v5 clients can be managed by one or more App-V v5 Servers, or by System Center 2012 Configuration Manager Service Pack 1, but they may not be managed by both at the same time. As such, when Configuration Manager deploys a virtual application it also removes the Publishing Servers from the App-V v5 client.
NOTE Configuration Manager does not remove the previously published Virtual Application Packages.
This behavior is by design.
App-V v5 ConfigMgr publishing server remove