I learned a few new things that might be useful for others:
My NetDuino Plus stopped deploying after I made some code changes. Could not get it to recover by unplugging, plugging, rebooting PC etc.
Turns out that I deployed something bad that makes the NetDuino hang.
To "fix" that - you just go to MFDeploy and click Erase and just erase the "app" and not the Firmware.
This allows me to instantly deploy again.
Now, weird thing is I manage to hang the netduino plus by creating a PWM for digital pin 1 and setting the duty cycle to 100. Anyways, this might be a known issue or something else I'm doing wrong...