I believe the issue is because the server has an open connection to the feature source in it's connection pool.
You can check this via the http://localhost/mapguide200x/mapagent/index.html pages and under Feature use GetFdoCacheInfo. If this lists a connection to your ODBC source for your database then you can't just overwrite the file.
I believe if you update the feature source by just opening it, entering the password and saving you will close and reopen the connection. You could try this after copying over your file.
Otherwise a server restart is required to close the connection or you would have to wait until the connection timeout has been reached.
Dave