FezConfig has this in advance menu -> reboot CLR.
But in your case I don’t think it works, because to reboot CLR, at least PC can communicate with the device, here is you can’t.
I uninstalled everything GHI and NETMF related and I followed the instructions from the link.
I skipped step one as I am using VS2010 and selected NETMF SDK 4.2 (RTM QFE2). The 3rd step seems to be a repeat of Step 2 but I downloaded that anyway and installed and selected the repair option on running setup.
Once this had all completed I connected my device (FEZ Hydra) my PC then discovered the device and installed the software, recognising the device as a FEZ Hydra.
I then opened the FEZ Config application and selected “Ping” and had the same error appear
I realised that step 2 and 3 were not the same download my explorer (or me) got confused with what had been downloaded as, when I went to run “my first project” from VS2010 I had an error because NETMF had not been installed. So I had to again repeat Step 2 and 3.
However after running through setups for the 3rd time now, still get the same error