I was recently trying to re-replicate a Storefront Server with another one after breaking the replication for upgrading Storefront version. After wiping the storefront config on the destination , replicating Failed with the event log

Failed to get the end status of the sever configuration update.
System.ServiceModel.FaultException, System.ServiceModel, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089
Physical path: C:\inetpub\wwwroot\Citrix\CitrixWeb associated with Virtual path: /Citrix/CitrixWeb is already in use.
at Citrix.DeliveryServices.ConfigurationReplication.WCF.ConfigurationReplication.EndUpdateConfiguration(IAsyncResult asyncResult)

Turns out the clear config powershell had not cleared the IIS Directory properly Deleting the storefront Dir below
C:\inetpub\wwwroot\Citrix\CitrixWeb Manually Fixed it