If your MyFTPHost host instance is configured to run on only one server, then you will only receive the file once.
The high availability solution is to cluster your Biztalk servers and have the MyFTPHost service fail-over if the server running your host instance fails. i.e. you have the MyFTPHost host instance configured on both servers but have it running on one and stopped on the other. The cluster software will manage starting and stopping each service as required.