After syncing the following error can occur in the Ektron Windows Service logs. 

An unexpected error occurred when applying batch file. Microsoft.Synchronization.ReplicaNotFoundException: Replica with the specified key was not found.

If you see the batch file error you may be able to resolve it by deleting the contents of the Ektron Windows Service's database folder. If you are using eSync be sure to delete on both sides of the sync. If Ektron load balancing is used, stop EWS on all load balanced servers at the same time, clear the files on all of the load balanced servers, and start EWS again. 

1. Stop the Ektron Windows Service. 
2. Clear the following folder. 
   C:\Program Files (x86)\Ektron\EktronWindowsService40\Database
3. Restart the Ektron Windows Service. 

If that fails, contact Application Support.