A Samba drive works like any other drive connected to the machine: for example Windows Explorer and drag and drop functionality are all available. Dragging a file onto a remote Eclipse project will add the file to the project and transfer the file to the server with correct CRLF settings.
If a project is created on a remote drive, the drive must be available for the project to open in Eclipse. If the drive is disconnected and off the network then the project will remain closed until the connection is reestablished.