I haven't experienced this, but I doubt the client would remove it's last configuration. In my understanding of VTP, the client will only change it's config by a server. Even if the server is offline, the client should be running it's last configuration.
Do a "show vtp status" and see when the last configuration was updated. This should help you out.
Be very careful when you add a new VTP server though. Because the new VTP server will have a newer update, it will overwrite all the clients configuration.
Also, you can have more than one server for redundancy. The vtp server with the newest configuration will be the one making the updates, and the other vtp server(s) will be update like a client from the master server.
-Bad Dos