EMC Testing is a real pain!
If your external hardware (at the end of your USB cable) has crashed and has no watchdog or similar to reset, I think there is little you can do at the PC end. If it is powered by the USB then it maybe be possible to remove the power and cause a reset, but I am afraid I don't know how to do this in software. I see you say that data was sent but not received, these seems odd.
It maybe usefull to look at preventing the noise from causing a problem in the first place. I have found that earthing is very important in EMC and it is worth trying to earth the cables at one end or the other or both and see what works best. I guess the hardware is not bought in, or you would not have to EMC test it, so you should be able to try this to some extent. You could also try to screen the cable in some way. We often use ferrite beads around the cables but I have never tried this on a USB cable.
One last thing, it is likely that during the EMC test your software will receive various illegal values so double check that they are all being handled correctly and it is not just that your application gets 'stuck' at some point, waiting for data that will never arrive.
Best of Luck