Close eclipse before shutting down, restart eclipse after resume. No, really - Windows disconnects remote drives during sleep: network adapter is suspended, thus disconnecting from the network, thus no more remote drives. During resume, the network stack takes more time to resume than the remote drive stack, thus no more remote drive.
I think you can mark the remote drive to be available when offline (http://windows.microsoft.com/en-au/windows-vista/working-with-network-files-when-you-are-offline), but I've never used this feature of Windows.