You have exported the server configuration of your FIM Synchronization server in order to install a new one.
Upon importing the old server configuration you are notified that you must refresh the interface of your Lotus Domino Connector.
In the event that you have true ECMA agents, you will note on the connectivity tab that there is a button to refresh the interfaces. This is not available on the ECMA 2.0-based Lotus Domino Connector.
The solution is very simple:
The Synchronization engine will notice that the DLL has changed and update the interfaces accordingly.